Genes from the 20Q13 amplicon and their uses

ABSTRACT

The present invention relates to cDNA sequences from a region of amplification on chromosome 20 associated with disease. The sequences can be used in hybridization methods for the identification of chromosomal abnormalities associated with various diseases. The sequences can also be used for treatment of diseases.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation-in-part of U.S. Ser. No. 08/785,532, filed on Jan. 17, 1997, U.S. Ser. No. 08/731,499 filed on Oct. 16, 1996 and U.S. Ser. No. 08/680,395 filed on Jul. 15, 1996, now U.S. Pat. No. 5,892,010 which is related to copending U.S. Patent Application, U.S. Ser. No. 08/546,130, filed Oct. 20, 1995, each of which is incorporated herein by reference for all purposes.

BACKGROUND OF THE INVENTION

This invention pertains to the field of cytogenetics. More particularly this invention pertains to the identification of genes in a region of amplification at about 20q13 in various cancers. The genes disclosed here can be used as probes specific for the 20q13 amplicon as well as for treatment of various cancers.

Chromosome abnormalities are often associated with genetic disorders, degenerative diseases, and cancer. In particular, the deletion or multiplication of copies of whole chromosomes or chromosomal segments, and higher level amplifications of specific regions of the genome are common occurrences in cancer. See, for example Smith, et al., Breast Cancer Res. Treat., 18: Suppl. 1: 5-14 (1991, van de Vijer & Nusse, Biochim. Biophys. Acta. 1072: 33-50(1991), Sato, et al., Cancer. Res., 50: 7184-7189 (1990). In fact, the amplification and deletion of DNA sequences containing proto-oncogenes and tumor-suppressor genes, respectively, are frequently characteristic of tumorigenesis. Dutrillaux, et al., Cancer Genet. Cytogenet., 49: 203-217 (1990). Clearly, the identification of amplified and deleted regions and the cloning of the genes involved is crucial both to the study of tumorigenesis and to the development of cancer diagnostics.

The detection of amplified or deleted chromosomal regions has traditionally been done by cytogenetics. Because of the complex packing of DNA into the chromosomes, resolution of cytogenetic techniques has been limited to regions larger than about 10 Mb; approximately the width of a band in Giemsa-stained chromosomes. In complex karyotypes with multiple translocations and other genetic changes, traditional cytogenetic analysis is of little utility because karyotype information is lacking or cannot be interpreted. Teyssier, J. R., Cancer Genet. Cytogenet., 37: 103 (1989). Furthermore, conventional cytogenetic banding analysis is time consuming, labor intensive, and frequently difficult or impossible.

More recently, cloned probes have been used to assess the amount of a given DNA sequence in a chromosome by Southern blotting. This method is effective even if the genome is heavily rearranged so as to eliminate useful karyotype information. However, Southern blotting only gives a rough estimate of the copy number of a DNA sequence, and does not give any information about the localization of that sequence within the chromosome.

Comparative genomic hybridization (CGH) is a more recent approach to identify the presence and localization of amplified/deleted sequences. See Kallioniemi, et al., Science, 258: 818 (1992). CGH, like Southern blotting, reveals amplifications and deletions irrespective of genome rearrangement. Additionally, CGH provides a more quantitative estimate of copy number than Souther blotting, and moreover also provides information of the localization of the amplified or deleted sequence in the normal chromosome.

Using CGH, the chromosomal 20q13 region has been identified as a region that is frequently amplified in cancers (see, e.g. Kallioniemi et al., Genomics, 20: 125-128 (1994)). Initial analysis of this region in breast cancer cell lines identified a region approximately 2 Mb on chromosome 20 that is consistently amplified.

SUMMARY OF THE INVENTION

The present invention relates to the identification of a narrow region (about 606 kb) within a 2 Mb amplicon located at about chromosome 20q13 (more precisely at 20q13.2) that is consistently amplified in primary tumors. In addition, this invention provides cDNA sequences from a number of genes which map to this region. These sequences are useful as probes or as probe targets for monitoring the relative copy number of corresponding sequences from a biological sample such as a tumor cell. Also provided is a contig (a series of clones that contiguously spans this amplicon) which can be used to prepare probes specific for the amplicon. The probes can be used to detect chromosomal abnormalities at 20q13.

Thus, in one embodiment, this invention provides a method of detecting a chromosome abnormality (e.g., an amplification or a deletion) at about position FLpter 0.825 on human chromosome 20 (20q13.2). The method involves contacting a chromosome sample from a patient with a composition consisting essentially of one or more labeled nucleic acid probes each of which binds selectively to a target polynucleotide sequence at about position FLpter 0.825 on human chromosome 20 under conditions in which the probe forms a stable hybridization complex with the target sequence; and detecting the hybridization complex. The step of detecting the hybridization complex can involve determining the copy number of the target sequence. The probe preferably comprises a nucleic acid that specifically hybridizes under stringent conditions to a nucleic acid selected from the nucleic acids disclosed here. Even more preferably, the probe comprises a subsequence selected from sequences set forth in SEQ. ID. Nos. 1-10 and 12. The probe is preferably labeled, and is more preferably labeled with digoxigenin or biotin. In one embodiment, the hybridization complex is detected in interphase nuclei in the sample. Detection is preferably carried out by detecting a fluorescent label (e.g., FITC, fluorescein, or Texas Red). The method can further involve contacting the sample with a reference probe which binds selectively to a chromosome 20 centromere.

This invention also provides for two new genes, ZABC1 and 1b1, in the 20q13.2 region that are both amplified and overexpressed in a variety of cancers. ZABC1 is a putative zinc finger protein. Zinc finger proteins are found in a variety of transcription factors, and amplification or overexpression of transcription factors typically results in cellular mis-regulation. ZABC1 and 1b1 thus appear to play an important role in the etiology of a number of cancers.

This invention provides for a new human cyclophilin nucleic acid (SEQ ID NO 13). Cyclophilin nucleic acids have been implicated in a variety of cellular processes, including signal transduction.

This invention also provides for proteins encoded by nucleic acid sequences in the 20q13 amplicon (SEQ. ID. Nos: 1-10 and 12-13) and subsequences, more preferably subsequences of at least 10 amino acids, preferably of at least 20 amino acids and most preferably of at least 30 amino acids in length. Particularly preferred subsequences are epitopes specific to the 20q13 proteins, more preferably epitopes specific to the ZABC1 and 1b1 proteins. Such proteins include, but are not limited to isolated polypeptides comprising at least 20 amino acids from a polypeptide encoded by the nucleic acids of SEQ. ID No. 1-10 and 12-13 or from the polypeptide of SEQ. ID. No. 11 wherein the polypeptide, when presented as an immunogen, elicits the production of an antibody which specifically binds to a polypeptide selected from the group consisting of a polypeptide encoded by the nucleic acids of SEQ. ID No. 1-10 and 12-13 or from the polypeptide of SEQ. ID. No. 11, where the polypeptide does not bind to antisera raised against a polypeptide selected from the group consisting of a polypeptide encoded by the nucleic acids of SEQ. ID No. 1-10 and 12-13 or from the polypeptide of SEQ. ID. No. 11 which has been fully immunosorbed with a polypeptide selected from the group consisting of a polypeptide encoded by the nucleic acids of SEQ. ID No. 1-10 and 12-13 or from the polypeptide of SEQ. ID. No. 11. In preferred embodiments, the polypeptides of the invention hybridize to antisera raised against a polypeptide encoded by those encoded by SEQ ID NOs. 1-13, where the antisera has been immunosorbed with the most structurally related previously known polypeptide. For example, a polypeptide of the invention binds to antisera raised against a polypeptide encoded by SEQ ID NO. 13, wherein the antisera has been immunosorbed with a rat or mouse cyclophilin polypeptide (Rat cyclophilin nucleic acids are known; see, GenBank™ under accession No. M19533; Mouse cyclophilin nucleic acids are known; see, GenBank™ under accession No. 50620. cDNAs from the mouse and rat cyclophilin cDNAs are about 85% identical to SEQ ID NO. 13).

In another embodiment, the method can involve detecting a polypeptide (protein) encoded by a nucleic acid (ORF) in the 20q13 amplicon. The method may include any of a number of well known protein detection methods including, but not limited to, the protein assays disclosed herein.

This invention also provides cDNA sequences from genes in the amplicon (SEQ. ID. Nos. 1-10 and 12-13). The nucleic acid sequences can be used in therapeutic applications according to known methods for modulating the expression of the endogenous gene or the activity of the gene product. Examples of therapeutic approaches include antisense inhibition of gene expression, gene therapy, monoclonal antibodies that specifically bind the gene products, and the like. The genes can also be used for recombinant expression of the gene products in vitro.

This invention also provides for proteins (e.g., SEQ. ID. No. 11) encoded by the cDNA sequences from genes in the amplicon (e.g., SEQ. ID. Nos. 1-10 and 12-13). Where the amplified nucleic acids include cDNA which are expressed, detection and/or quantification of the protein expression product can be used to identify the presence or absence or quantify the amplification level of the amplicon or of abnormal protein products produced by the amplicon.

The probes disclosed here can be used in kits for the detection of a chromosomal abnormality at about position FLpter 0.825 on human chromosome 20. The kits include a compartment which contains a labeled nucleic acid probe which binds selectively to a target polynucleotide sequence at about FLpter 0.825 on human chromosome 20. The probe preferably includes at least one nucleic acid that specifically hybridizes under stringent conditions to a nucleic acid selected from the nucleic acids disclosed here. Even more preferably, the probes comprise one or more nucleic acids selected from the nucleic acids disclosed here. In a preferred embodiment, the probes are labeled with digoxigenin or biotin. The kit may further include a reference probe specific to a sequence in the centromere of chromosome 20.

Definitions

A “nucleic acid sample” as used herein refers to a sample comprising DNA in a form suitable for hybridization to a probes of the invention. The nucleic acid may be total genomic DNA, total mRNA, genomic DNA or mRNA from particular chromosomes, or selected sequences (e.g. particular promoters, genes, amplification or restriction fragments, cDNA, etc.) within particular amplicons disclosed here. The nucleic acid sample may be extracted from particular cells or tissues. The tissue sample from which the nucleic acid sample is prepared is typically taken from a patient suspected of having the disease associated with the amplification being detected. In some cases, the nucleic acids may be amplified using standard techniques such as PCR, prior to the hybridization. The sample may be isolated nucleic acids immobilized on a solid surface (e.g., nitrocellulose) for use in Southern or dot blot hybridizations and the like. The sample may also be prepared such that individual nucleic acids remain substantially intact and comprises interphase nuclei prepared according to standard techniques. A “nucleic acid sample” as used herein may also refer to a substantially intact condensed chromosome (e.g. a metaphase chromosome). Such a condensed chromosome is suitable for use as a hybridization target in in situ hybridization techniques (e.g. FISH). The particular usage of the term “nucleic acid sample” (whether as extracted nucleic acid or intact metaphase chromosome) will be readily apparent to one of skill in the art from the context in which the term is used. For instance, the nucleic acid sample can be a tissue or cell sample prepared for standard in situ hybridization methods described below. The sample is prepared such that individual chromosomes remain substantially intact and typically comprises metaphase spreads or interphase nuclei prepared according to standard techniques.

A “chromosome sample” as used herein refers to a tissue or cell sample prepared for standard in situ hybridization methods described below. The sample is prepared such that individual chromosomes remain substantially intact and typically comprises metaphase spreads or interphase nuclei prepared according to standard techniques.

“Nucleic acid” refers to a deoxyribonucleotide or ribonucleotide polymer in either single- or double-stranded form, and unless otherwise limited, would encompass known analogs of natural nucleotides that can function in a similar manner as naturally occurring nucleotides.

An “isolated” polynucleotide is a polynucleotide which is substantially separated from other contaminants that naturally accompany it, e.g., protein, lipids, and other polynucleotide sequences. The term embraces polynucleotide sequences which have been removed or purified from their naturally-occurring environment or clone library, and include recombinant or cloned DNA isolates and chemically synthesized analogues or analogues biologically synthesized by heterologous systems.

“Subsequence” refers to a sequence of nucleic acids that comprise a part of a longer sequence of nucleic acids.

A “probe” or a “nucleic acid probe”, as used herein, is defined to be a collection of one or more nucleic acid fragments whose hybridization to a target can be detected. The probe may be unlabeled or labeled as described below so that its binding to the target can be detected. The probe is produced from a source of nucleic acids from one or more particular (preselected) portions of the genome, for example one or more clones, an isolated whole chromosome or chromosome fragment, or a collection of polymerase chain reaction (PCR) amplification products. The probes of the present invention are produced from nucleic acids found in the 20q13 amplicon as described herein. The probe may be processed in some manner, for example, by blocking or removal of repetitive nucleic acids or enrichment with unique nucleic acids. Thus the word “probe” may be used herein to refer not only to the detectable nucleic acids, but to the detectable nucleic acids in the form in which they are applied to the target, for example, with the blocking nucleic acids, etc. The blocking nucleic acid may also be referred to separately. What “probe” refers to specifically is clear from the context in which the word is used.

The probe may also be isolated nucleic acids immobilized on a solid surface (e.g., nitrocellulose). In some embodiments, the probe may be a member of an array of nucleic acids as described, for instance, in WO 96/17958. Techniques capable of producing high density arrays can also be used for this purpose (see, e.g., Fodor et al. Science 767-773 (1991) and U.S. Pat. No. 5,143,854).

“Hybridizing” refers the binding of two single stranded nucleic acids via complementary base pairing.

“Bind(s) substantially” or “binds specifically” or “binds selectively” or “hybridizes specifically” refer to complementary hybridization between an oligonucleotide and a target sequence and embraces minor mismatches that can be accommodated by reducing the stringency of the hybridization media to achieve the desired detection of the target polynucleotide sequence. These terms also refer to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent conditions when that sequence is present in a complex mixture (e.g., total cellular) DNA or RNA. The term “stringent conditions” refers to conditions under which a probe will hybridize to its target subsequence, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. “Stringent hybridization” and “Stringent hybridization wash conditions” in the context of nucleic acid hybridization experiments such as CGH, FISH, Southern and northern hybridizations are sequence dependent, and are different under different environmental parameters. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology-Hybridization with Nucleic Acid Probes part I chapter 2 “overview of principles of hybridization and the strategy of nucleic acid probe assays”, Elsevier, N.Y. Generally, highly stringent hybridization and wash conditions are selected to be about 5° C. lower than the thermal melting point (T_(m)) for the specific sequence at a defined ionic strength and ph. The T_(m) is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Very stringent conditions are selected to be equal to the T_(m) for a particular probe.

An example of stringent hybridization conditions for hybridization of complementary nucleic acids which have more than 100 complementary residues on a filter in a Southern or northern blot is 50% formalin with 1 mg of heparin at 42° C., with the hybridization being carried out overnight. An example of stringent wash conditions is a 0.2×SSC wash at 65° C. for 15 minutes (see, Sambrook, supra for a description of SSC buffer). Often, the high stringency wash is preceded by a low stringency wash to remove background probe signal. An example medium stringency wash for a duplex of, e.g., about 100 nucleotides or more, is 1×SSC at 45° C. for 15 minutes. An example low stringency wash for a duplex of, e.g., more than 100 nucleotides, is 4×SSC at 40° C. for 15 minutes. In general, a signal to noise ratio of 2× (or higher) than that observed for an unrelated probe in the particular hybridization assay indicates detection of a specific hybridization.

One of skill will recognize that the precise sequence of the particular probes described herein can be modified to a certain degree to produce probes that are “substantially identical” to the disclosed probes, but retain the ability to bind substantially to the target sequences. Such modifications are specifically covered by reference to the individual probes herein. The term “substantial identity” of polynucleotide sequences means that a polynucleotide comprises a sequence that has at least 90% sequence identity, more preferably at least 95%, compared to a reference sequence using the methods described below using standard parameters.

Two nucleic acid sequences are said to be “identical” if the sequence of nucleotides in the two sequences is the same when aligned for maximum correspondence as described below. The term “complementary to” is used herein to mean that the complementary sequence is identical to all or a portion of a reference polynucleotide sequence. Nucleic acids which do not hybridize to complementary versions of each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical. This occurs, e.g., when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code.

Sequence comparisons between two (or more) polynucleotides are typically performed by comparing sequences of the two sequences over a “comparison window” to identify and compare local regions of sequence similarity. A “comparison window”, as used herein, refers to a segment of at least about 20 contiguous positions, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned.

Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman Adv. Appl. Math. 2: 482 (1981), by the homology alignment algorithm of Needleman and Wunsch J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson and Lipman Proc. Natl. Acad. Sci. (U.S.A.) 85: 2444 (1988), by computerized implementations of these algorithms.

“Percentage of sequence identity” is determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. Another indication that nucleotide sequences are substantially identical is if two molecules hybridize to the same nucleic acid sequence under stringent conditions.

“Conservatively modified variations” of a particular nucleic acid sequence refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given polypeptide. For instance, the codons CGU, CGC, CGA, CGG, AGA, and AGG all encode the amino acid arginine. Thus, at every position where an arginine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are “silent variations,” which are one species of “conservatively modified variations.” Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation. One of skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine) can be modified to yield a functionally identical molecule by standard techniques. Accordingly, each “silent variation” of a nucleic acid which encodes a polypeptide is implicit in each described sequence. Furthermore, one of skill will recognize that individual substitutions, deletions or additions which alter, add or delete a single amino acid or a small percentage of amino acids (typically less than 5%, more typically less than 1%) in an encoded sequence are “conservatively modified variations” where the alterations result in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. The following six groups each contain amino acids that are conservative substitutions for one another:

1) Alanine (A), Serine (S), Threonine (M);

2) Aspartic acid (D), Glutamic acid (E);

3) Asparagine (N), Glutamine (Q);

4) Arginine (R), Lysine (K);

5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and

6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).

The term “20q13 amplicon protein” is used herein to refer to proteins encoded by ORFs in the 20q13 amplicon disclosed herein. Assays that detect 20q13 amplicon proteins are intended to detect the level of endogenous (native) 20q13 amplicon proteins present in subject biological sample. However, exogenous 20q13 amplicon proteins (from a source extrinsic to the biological sample) may be added to various assays to provide a label or to compete with the native 20q13 amplicon protein in binding to an anti-20q13 amplicon protein antibody. One of skill will appreciate that a 20q13 amplicon protein mimetic may be used in place of exogenous 20q13 protein in this context. A “20q13 protein”, as used herein, refers to a molecule that bears one or more 20q13 amplicon protein epitopes such that it is specifically bound by an antibody that specifically binds a native 20q13 amplicon protein.

As used herein, an “antibody” refers to a protein consisting of one or more polypeptides substantially encoded by immunoglobulin genes or fragments of immunoglobulin genes. The recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon and mu constant region genes, as well as the myriad immunoglobulin variable region genes. Light chains are classified as either kappa or lambda. Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively.

The basic immunoglobulin (antibody) structural unit is known to comprise a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kD) and one “heavy” chain (about 50-70 kD). The N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The terms variable light chain (V_(L)) and variable heavy chain (V_(H)) refer to these light and heavy chains respectively.

Antibodies may exist as intact immunoglobulins or as a number of well characterized fragments produced by digestion with various peptidases. Thus, for example, pepsin digests an antibody below the disulfide linkages in the hinge region to produce F(ab)′₂, a dimer of Fab which itself is a light chain joined to V_(H)-C_(H)1 by a disulfide bond. The F(ab)′₂ may be reduced under mild conditions to break the disulfide linkage in the hinge region thereby converting the F(ab)′₂ dimer into an Fab′ monomer. The Fab′ monomer is essentially an Fab with part of the hinge region (see, Fundamental Immunology, W. E. Paul, ed., Raven Press, N.Y. (1993) for a more detailed description of other antibody fragments). While various antibody fragments are defined in terms of the digestion of an intact antibody, one of skill will appreciate that such Fab′ fragments may be synthesized de novo either chemically or by utilizing recombinant DNA methodology. Thus, the term antibody, as used herein also includes antibody fragments either produced by the modification of whole antibodies or synthesized de novo using recombinant DNA methodologies.

The phrase “specifically binds to a protein” or “specifically immunoreactive with”, when referring to an antibody refers to a binding reaction which is determinative of the presence of the protein in the presence of a heterogeneous population of proteins and other biologics. Thus, under designated immunoassay conditions, the specified antibodies bind to a particular protein and do not bind in a significant amount to other proteins present in the sample. Specific binding to a protein under such conditions may require an antibody that is selected for its specificity for a particular protein. For example, antibodies can be raised to the a 20q13 amplicon protein that bind the 20q13 amplicon protein and not to any other proteins present in a biological sample. A variety of immunoassay formats may be used to select antibodies specifically immunoreactive with a particular protein. For example, solid-phase ELISA immunoassays are routinely used to select monoclonal antibodies specifically immunoreactive with a protein. See Harlow and Lane (1988) Antibodies, A Laboratory Manual, Cold Spring Harbor Publications, New York, for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1(A) shows disease-free survival of 129 breast cancer patients according to the level of 20q13 amplification. Patients with tumors having high level 20q13 amplification have a shorter disease-free survival (p=0.04 by Mantel-Cox test) compared to those having no or low level amplification.

FIG. 1(B) Shows the same disease-free survival difference of FIG. 1(A) in the subgroup of 79 axillary node-negative patients (p=0.0022 by Mantel-Cox test).

FIG. 2 shows a comparison of 20q13 amplification detected by FISH in a primary breast carcinoma and its metastasis from a 29-year patient. A low level amplification of 20q13 (20q13 compared to 20p reference probe) was found in the primary tumor. The metastasis, which appeared 8 months after mastectomy, shows a high level amplification of the chromosome 20q13 region. The overall copy number of chromosome 20 (20p reference probe) remained unchanged. Each data point represents gene copy numbers in individual tumor cells analyzed.

FIG. 3 shows a graphical representation of the molecular cytogenetic mapping and subsequent cloning of the 20q13.2 amplicon. Genetic distance is indicated in centiMorgans (cM). The thick black bar represents the region of highest level amplification in the breast cancer cell line BT474 and covers a region of about 1.5 Mb. P1 and BAC clones are represented as short horizontal lines and YAC clones as heavier horizontal lines. Not all YAC and P1 clones are shown. YACs 957f3, 782c9, 931h12, and 902 are truncated. Sequence tagged sites (STSs) appear as thin vertical lines and open circles indicate that a given YAC has been tested for and is positive for a given STS. Not all STSs have been tested on all YACs. The interval from which more than 100 exons have been trapped is represented as a filled box. The 600 kb interval spanning the region of highest amplification level in primary tumors is represented by the filled black box (labeled Sequence). The lower part of the figure shows the levels of amplification in two primary tumors that further narrow the region of highest amplification to within about 600 kb.

FIG. 4 provides a higher resolution map of the amplicon core as defined in primary tumors.

FIG. 5 shows the map location of 15 genes in the amplicon.

FIG. 6 shows a sequence alignment between Rat cyclophiilin (SEQ ID NOS: 14, 15, 16, and 17) and SEQ ID 13 (SEQ ID NOS: 18, 19, 20, and 21).

FIG. 7 is a physical map of the 20q13 amplicon. Row A of the figure shows the position of STSs used to assemble the map. Row B shows the position of YACs. Row C shows the position of P1 and BAC clones. Row D shows the position of trapped exons, direct selected cDNAs, ESTs, and genes. Row E shows results of hybridization analysis of various primary tumors and cell lines using P1 or BAC clones as noted there. A solid black circle indicates high amplification, a shaded circle indicates intermediate amplification and an open circle indicates no amplification as detected by each of the clones.

DETAILED DESCRIPTION

This invention provides a number of cDNA sequences which can be used as probes for the detection of chromosomal abnormalities at 20q13. Studies using comparative genomic hybridization (CGH) have shown that a region at chromosome 20q13 is increased in copy number frequently in cancers of the breast (˜30%), ovary (˜15%), bladder (˜30%), head and neck (˜75%) and colon (˜80%). This suggests the presence of one or more genes that contribute to the progression of several solid tumors are located at 20q13.

Gene amplification is one mechanism by which dominantly acting oncogenes are overexpressed, allowing tumors to acquire novel growth characteristics and/or resistance to chemotherapeutic agents. Loci implicated in human breast cancer progression and amplified in 10-25% of primary breast carcinomas include the erbB-2 locus (Lupu et al., Breast Cancer Res. Treat., 27: 83 (1993), Slamon et al. Science, 235: 177-182 (1987), Heiskanen et al. Biotechniques, 17: 928 (1994)) at 17q12, cyclin-D (Mahadevan et al., Science, 255: 1253-1255 (1993), Gillett et al., Canc. Res., 54: 1812 (1994)) at 11q13 and MYC (Gaffey et al., Mod. Pathol., 6: 654 (1993)) at 8q34.

Pangenomic surveys using comparative genomic hybridization (CGH) recently identified about 20 novel regions of increased copy number in breast cancer (Kallioniemi et al., Genomics, 20: 125-128 (1994)). One of these loci, band 20q13, was amplified in 18% of primary tumors and 40% of cell lines (Kallioniemi et al., Genomics, 20: 125-128 (1994)). More recently, this same region was found amplified in 15% of ovarian, 80% of bladder and 80% of colorectal tumors. The resolution of CGH is limited to 5-10 Mb. Thus, FISH was performed using locus specific probes to confirm the CGH data and precisely map the region of amplification.

The 20q13 region has been analyzed in breast cancer at the molecular level and a region, approximately 600 kb wide, that is consistently amplified was identified, as described herein. Moreover, as shown herein, the importance of this amplification in breast cancer is indicated by the strong association between amplification and decreased patient survival and increased tumor proliferation (specifically, increased fraction of cells in S-phase).

In particular, as explained in detail in Example 1, high-level 20q13 amplification was associated (p=0.0022) with poor disease free survival in node-negative patients, compared to cases with no or low-level amplification (FIG. 1). Survival of patients with moderately amplified tumors did not differ significantly from those without amplification. Without being bound to a particular theory, it is suggested that an explanation for this observation may be that low level amplification precedes high level amplification. In this regard, it may be significant that one patient developed a local metastasis with high-level 20q13.2 amplification 8 month after resection of a primary tumor with low level amplification (FIG. 2).

The 20q13 amplification was associated with high histologic grade of the tumors. This correlation was seen in both moderately and highly amplified tumors. There was also a correlation (p=0.0085) between high level amplification of a region complementary to a particular probe, RMC20C001 (Tanner et al., Cancer Res., 54: 4257-4260 (1994)), and cell proliferation, measured by the fraction of cells in S-phase. This finding is important because it identifies a phenotype that can be scored in functional assays, without knowing the mechanism underlying the increased S-phase fraction. The 20q13 amplification did not correlate with the age of the patient, primary tumor size, axillary nodal or steroid hormone-receptor status.

This work localized the 20q13.2 amplicon to an interval of approximately 2 Mb. Furthermore, it suggests that high-level amplification, found in 7% of the tumors, confers an aggressive phenotype on the tumor, adversely affecting clinical outcome. Low level amplification (22% of primary tumors) was associated with pathological features typical of aggressive tumors (high histologic grade, aneuploidy and cell proliferation) but not patient prognosis.

In addition, it is shown herein that the 20q13 amplicon (more precisely the 20q13.2 amplicon) is one of three separate co-amplified loci on human chromosome 20 that are packaged together throughout the genomes of some primary tumors and breast cancer cell lines. No known oncogenes map in the 20q13.2 amplicon.

Identification of 20q13 Amplicon Probes.

Initially, a paucity of available molecular cytogenetic probes dictated that FISH probes be generated by the random selection of cosmids from a chromosome 20 specific library, LA20NC01, and then mapped them to chromosome 20 by digital imaging microscopy. Approximately 46 cosmids, spanning the 70 Mb chromosome, were isolated for which fractional length measurements (FLpter) and band assignments were obtained. Twenty six of the cosmids were used to assay copy number in the breast cancer cell line BT474 by interphase FISH analysis. Copy number was determined by counting hybridization signals in interphase nuclei. This analysis revealed that cosmid RMC20C01 (FLpter, 0.824; 20q13.2), described by Stokke et al., Genomics, 26: 134-137 (1995), defined the highest-level amplification (^(˜)60 copies/cell) in BT474 cells (Tanner et al., Cancer Res., 54: 4257-4260 (1994)).

P1 clones containing genetically mapped sequences were selected from 20q13.2 and used as FISH probes to confirm and further define the region of amplification. Other P1 clones were selected for candidate oncogenes broadly localized to the 20q13.2 region (Flpter, 0.81-0.84). These were selected from the DuPont P1 library (Shepherd, et al., Proc. Natl. Acad. Sci. USA, 92: 2629 (1994), available commercially from Genome Systems), by PCR (Saiki et al, Science, 230: 1350 (1985)) using primer pairs developed in the 3′ untranslated region of each candidate gene. Gene specific P1 clones were obtained for, protein tyrosine phosphatase (PTPN1, Flpter 0.78), melanocortin 3 receptor (MC3R, Flpter 0.81), phosphoenolpyruvate carboxy kinase (PCK1, Flpter 0.85), zinc finger protein 8 (ZNF8, Flpter 0.93), guanine nucleotide-binding protein (GNAS 1, Flpter 0.873), src-oncogene (SRC, Flpter 0.669), topoisomerase 1 (TOP1, Flpter 0.675), the bcl-2 related gene bcl-x (Flpter 0.526) and the transcription factor E2F-1 (FLpter 0.541). Each clone was mapped by digital imaging microscopy and assigned Flpter values. Five of these genes (SRC, TOPO1, GNAS1, E2F-1 and BC1-x) were excluded as candidate oncogenes in the amplicon because they mapped well outside the critical region at Flpter 0.81-0.84. Three genes (PTPNR1, PCK-1 and MC3R) localized close enough to the critical region to warrant further investigation.

Interphase FISH on 14 breast cancer cell lines and 36 primary tumors using 24 cosmid and 3 gene specific P1 (PTPNRL, PCK-1 and MC3R) probes found high level amplification in 35% (5/14) of breast cancer cell lines and 8% (3/36) of primary tumors with one or more probe. The region with the highest copy number in 4/5 of the cell lines and 3/3 primary tumors was defined by the cosmid RMC20C001. This indicated that PTPNR1, PCK1 and MC3R could also be excluded as candidates for oncogenes in the amplicon and, moreover, narrowed the critical region from 10 Mb to 1.5-2.0 Mb (see, Tanner et al., Cancer Res., 54: 4257-4260 (1994).

Because probe RMC20C001 detected high-level (3 to 10-fold) 20q13.2 amplification in 35% of cell lines and 8% of primary tumors it was used to (1) define the prevalence of amplification in an expanded tumor population, (2) assess the frequency and level of amplification in these tumors, (3) evaluate the association of the 20q13.2 amplicon with pathological and biological features, (4) determine if a relationship exists between 20q13 amplification and clinical outcome and (5) assess 20q13 amplification in metastatic breast tumors.

As detailed in Example 1, fluorescent in situ hybridization (FISH) with RMC20C001 was used to assess 20q13.2 amplification in 132 primary and 11 recurrent breast tumors. The absolute copy number (mean number of hybridization signals per cell) and the level of amplification (mean number of signals relative to the p-arm reference probe) were determined. Two types of amplification were found: Low level amplification (1.5-3 fold with FISH signals dispersed throughout the tumor nuclei) and high level amplification (>3 fold with tightly clustered FISH signals). Low level 20q13.2 amplification was found in 29 of the 132 primary tumors (22%), whereas nine cases (6.8%) showed high level amplification.

RMC20C001 and four flanking P1 probes (MC3R, PCK, RMC20C026, and RMC20C030) were used to study the extent of DNA amplification in highly amplified tumors. Only RMC20C001 was consistently amplified in all tumors. This finding confirmed that the region of common amplification is within a 2 Mb interval flanked by but not including PCK-1 and MC3R.

A physical map was assembled to further localize the minimum common region of amplification and to isolate the postulated oncogene(s). The DuPont P1 library (Shepherd et al. Proc. Natl. Acad. Sci. USA, 91: 2629 (1994) was screened for STSs likely to map in band 20q13.2. P1 clones at the loci D20S102, D20S100, D20S120, D20S183, D20S480, D20S211 were isolated, and FISH localized each to 20q13.2. Interphase FISH analysis was then performed in the breast cancer cell line BT474 to assess the amplification level at each locus. The loci D20S100-D20S120-D20S183-D20S480-D20S211 were highly amplified in the BT474 cell line, whereas D20S102 detected only low level amplification. Therefore, 5 STSs, spanning 5 cM, were localized within the 20q13.2 amplicon and were utilized to screen the CEPH megaYAC library.

CEPH megaYAC library screening and computer searches of public databases revealed D20S120-D20S183-D20S480-D20S211 to be linked on each of three megaYAC clones y820f5, 773h10, and 931h6 (FIG. 3). Moreover, screening the CEPH megaYAC library with STSs generated from the ends of cosmids RMC20C001, RMC20C30 and RMC20C028 localized RMC20C001 to each of the same three YAC clones. It was estimated, based on the size of the smallest of these YAC clones, that D20S120-D20S183-RMC20C001-D20S480-D20S211 map into an interval of less than 1.1 Mb. D20S100 was localized 300 kb distal to D20S120 by interphase FISH and to YAC901b12 by STS mapping. The combined STS data made it possible to construct a 12 member YAC contig which spans roughly 4 Mb encompassing the 1.5 Mb amplicon and containing the loci RMC20C030-PCK1-RMC20C001-MC3R-RMC20C026. Each YAC was mapped by FISH to confirm localization to 20q13.2 and to check for chimerism. Five clonal isolates of each YAC were sized by pulsed field gel electrophoresis (PFGE). None of the YACs are chimeric, however, several are highly unstable.

The YAC contig served as a framework from which to construct a 2 MbP1 contig spanning the 20Q13 amplicon. P1 clones offered numerous advantages over YAC clones including (1) stability, (2) a chimeric frequency of less than 1% (3) DNA isolation by standard miniprep procedures, (4) they make ideal FISH probes, (5) the ends can be sequenced directly, (6) engineered γδ transposons carrying bidirectional primer binding sites can be integrated at any position in the cloned DNA (Strathmann et al., Proc. Natl. Acad. Sci. USA, 88: 1247 (1991)) (7) P1 clones are the templates for sequencing the human and Drosophila genomes at the LBNL HGC (Palazzolo et al. DOE Human Genome Program, Contractor-Grantee Workhop IV. Santa Fe, N.Mex. Nov. 13-17 1994).

About 90 P1 clones were isolated by screening the DuPont P1 library either by PCR or filter hybridization. For PCR based screening, more than 22 novel STSs were created by two methods. In the first method, the ends of P1 clones localized to the amplicon were sequenced, STSs developed, and the P1 library screened for walking clones. In the second approach inter-Alu PCR (Nelson et al., 86: 6686-6690 (1989)) was performed on YACs spanning the amplicon and the products cloned and sequenced for STS creation. In the filter based hybridization scheme P1 clones were obtained by performing inter-Alu PCR on YACs spanning the amplicon, radio-labeling the products and hybridizing these against filters containing a gridded array of the P1 library. Finally, to close gaps a human genomic bacterial artificial chromosome (BAC) library (Shizuya et al. Proc. Natl. Acad. Sci. USA, 89: 8794 (1992), commercially available from Research Genetics, Huntsville, Ala., USA) was screened by PCR. These methods combined to produce more than 100 P1 and BAC clones were localized to 20q13.2 by FISH. STS content mapping, fingerprinting, and free-chromatin fish (Heiskanen et al., BioTechniques, 17: 928 (1994)) were used to construct the 2 Mb contig shown in FIG. 3 as well as in FIG. 4. FIG. 7 is a second physical map of the region showing a minimum tiling contig.

Fine Mapping the 20q13.2 Amplicon in BT474

Clones from the 2 Mb P1 contig were used with FISH to map the level of amplification at 20q13.2 in the breast cancer cell line BT474. 35 P1 probes distributed at regular intervals along the contig were used. The resulting data indicated that the region of highest copy number increase in BT474 occurs between D20S100 and D20S211, an interval of approximately 1.5 Mb. P1 FISH probes, in this interval, detect an average of 50 signals per interphase nuclei in BT474, while no, or only low level amplification, was detected with the P1 clones outside this region. Thus, both the proximal and distal boundaries of the amplicon were cloned.

Fine Mapping the 20q13.2 Amplicon in Primary Tumors.

Fine mapping the amplicon in primary tumors revealed the minimum common region of high amplification (MCA) that is of pathobiological significance. This process is analogous to screening for informative meiosis in the narrowing of genetic intervals encoding heritable disease genes. Analysis of 132 primary tumors revealed thirty-eight primary tumors that are amplified at the RMC20C001 locus. Nine of these tumors have high level amplification at the RMC20C001 locus and were further analyzed by interphase FISH with 8 P1s that span the ≈2 Mb contig. The minimum common region of amplification (MCA) was mapped to a ≈600 kb interval flanked by P1 clones #3 and #12 with the highest level of amplification detected by P1 clone #38 corresponding to RMC20C001 (FIGS. 3 and 7).

The P1 and BAC clones spanning the 600 kb interval of the 20q13 amplicon are listed in Tables 1 and 2 which provide a cross-reference to the DuPont P1 library described by Shepherd, et al., Proc. Natl. Acad. Sci. USA, 92: 2629 (1994). These P1 and BAC probes are available commercially from Genetic Systems, and Research Genetics, respectively).

TABLE I Cross reference to probes of the DuPont P1 library (Shepherd, et al., Proc. Natl. Acad. Sci. USA, 92:2629 (1994) which is commercially available from Genomic Systems, St. Louis, Missouri, USA). PCR primers are illustrated for amplificatiom of Sequence tag sites for each clone. In addition, PCR conditions (Mg concentration and annealing temperature), as well as PCR product size, is provided. Size: PCR product Size; mM MgCl: Mg concentration; Ann.: Annealing temperature; P1: P1 probe ID number; PC: DuPont Library Plate Coordinates; SCA: DuPont Library Single Clone address; SEQ-forward and SEQ-backward: forward and backward PCR primers, respectively; SEQ ID NO:-forward and SEQ ID NO:-backward: Sequence Listing SEQ ID NO: for forward and backward primers, respectively. SEQ ID SEQ ID PRIMER SIZE mM NO NO:- NAME (bp) MgCl Ann. P1 PC SCA SEQ-forward SEQ-backward forward backward 352.32 136 1.5 52 20 103-e5 1228e TTGGCATTGGTAT TTGGAGCAGAGA 22 23 CAGGTAGCTG GGGGATTGTGTG 388.13 201 1.5 52 17 69g6 821 AATCCCCTCAAAC TGGAGCCTGAACT 24 25 F1/B1 CCTGCTGCTAC TCTGCAATC 19 98f4 1167f AATCCCCTCAAAC TGGAGCCTGAACT ″ ″ CCTGCTGCTAC TCTGCAATC D20S183 270 3 48 30 124g6 CCGGGATACCGAC TGCACATAAAAC 26 27 ATTG AGCCAGC 40 24h1 276h CCGGGATACCGAC TGCACATAAAAC ″ ″ D20S211 135 1.5 52 29 119f4 1418f TTGGAATCAATGG AGCTTFACCCAAT 28 29 ½ AGCAAAA GTGGTCC D20S480 300 3 55 68 100d12 1199d2 GTGGTGAACACCA AAGCAAATAAAA 30 31 ATAAATGG CCAATAAACTCG 41 86c1 1020c GTGGTGAACACCA AAGCAAATAAAA ″ ″ ATAAATGG CCAATAAACTCG 42 103d9 1232d GTGGTGAACACCA AAGCAAATAAAA ″ ″ ATAAATGG CCAATAAACTCG 67 91b2 1081b9 GTGGTGAACACCA AAGCAAATAAAA ″ ″ ATAAATGG CCAATAAACTCG 9X-SP6 165 1.5 55 7 31d11 370d CAAGATCTGACCC GACTTCTTCAGGA 32 33 hmF/hmB CGTCAATC AAGAGATCAGTG 9 3519 416f CAAGATCTGACCC GACTTCTTCAGGA ″ ″ CGTCAATC AAGAGATCAGTG 11S-17 146 3 58 11 41b1 480b GCCATGTACCCAC TCAGAACACCCGT 34 35 F2/B4 CTGAAAAATC GCAGAATTAAG 12T-T7 153 3 58 12 42c2 493c CCTAAAACTTGGT GTCTCACAAGGCA 36 37 F2/B1 GCTTAAATCTA GATGTGG 28T 219 1.5 52 74 888f2 TTTGTGTATGTTG CTTCCAATCTCAT 38 39 F1/B1 AGCCATC TCTATGAGG 2 12c6 137c TTTGTGTATGTTG CTTCCAATCTCAT ″ ″ AGCCATC TCTATGAGG 25 118c11 1413c TTTGTGTATGTTG CTTCCAATCTCAT ″ ″ AGCCATC TCTATGAGG 26 118c11 1413c TTTGTGTATGTTG CTTCCAATCTCAT ″ ″ AGCCATC TCTATGAGG 28S 214 1.5 55 28 118g11 1413g GCTTGTTTAAGTG CACTCTGGTAAAT 40 41 F1/B3 TCACTAGGG GACCTTTGTC 25 118c11 1413c GCTTGTTTAAGTG CACTCTGGTAAAT ″ ″ TCACTAGGG GACCTTTGTC 27 118g11 1413g GCTTGTTTAAGTG CACTCTGGTAAAT ″ ″ TCACTAGGG GACCTTTGTC 10 36f10 429f GCTTGTTTAAGTG CACTCTGGTAAAT ″ ″ TCACTAGGG GACCTTTGTC 69S 100 3 55 69 412b5 CCTACACCATTCC GCCAGATGTATGT 42 43 AACTTTGG TTGCTACGGAAC 5 23c1 264c CCTACACCATTCC GCCAGATGTATGT ″ ″ AACTTTGG TTGCTACGGAAC HSCOFH 129 1.5 55 3 12-e11 142e TCTCAAACCTGTC CTGCTGTGGTGGA 44 45 032 F/B CACTTCTTG GAATGG 18 77a10 921a TCTCAAACCTGTC CTGCTGTGGTGGA ″ ″ CACTTCTTG GAATGG 60A1 191 1.5 58 36 112g8 1139g TGTCCTCCTTCTC AATGCCTCCACTC 46 47 CCTCATCCTAC ACAGGAATG 39 34a6 401a TGTCCTCCTTCTC AATGCCTCCACTC ″ ″ CCTCATCCTAC ACAGGAATG 820F5A1 175 1.5 48 15 53c7 630c CCTCTTCAGTGTC GGGAGGAGGTTG 48 49 T F1/B1 TTCCTATTGA TAGGCAAC 16 58b9 692b CCTCTTCAGTGTC GGGAGGAGGTTG ″ ″ TTCCTATTGA TAGGCAAC 10311f33 185 1141 T7F3/B3 D7

TABLE 2 Cross reference to probes of the BAC library. Clone # refers to the clone number provided, e.g., in FIGS. 3, 4 and 7, while the plate coordinates are the plate coordinates in the Research Genetics BAC library. Size: PCR product Size; mM MgCl: Mg concentration; Ann.: Annealing temperature; BAC #: BAC probe ID number; SEQ-forward and SEQ-backward: forward and backward PCR primers, respectively; SEQ ID NO:-forward and SEQ ID NO:- backward: Sequence Listing SEQ ID NO: for forward and backward primers, respectively. SEQ ID SEQ ID PRIMER SIZE mM BAC BAC Plate NO. NO. NAME (bp) MgCl Ann. # Coordinates SEQ-forward SEQ-backward forward backward 18T F1/B1 156 3 62  99 L11 plate AGCAAAGCAAA TGACATGGGAGA 50 51 146 GGTGGCACAC AGACACACTTCC 9S F1/B1 214 1.5 55  97 E8 plate 183 AGGTTTACCAAT TCTACATCCCAT 52 53 GTGTTTGG TCTCTTCTG D20S480 300 3 55  95 H15 plate GTGGTGAACACC AAGCAAATAAAA 54 55 140 AATAAATGG CCAATAAACTCG D20S211 135 1.5 52 103 A15 plate TTGGAATCAATG AGCTTTACCCAA 56 57 ½ 188 GAGCAAAA TGTGGTCC 102 A1 plate 46 TTGGAATCAATG AGCTTTACCCAA ″ ″ GAGCAAAA TGTGGTCC 11S-17 146 3 58 100 E4 plate 43 GCCATGTACCCA TCAGAACACCCG 58 59 F2/B4 CCTGAAAAATC TGCAGAATTAAG 101 J5 plate 118 GCCATGTACCCA TCAGAACACCCG ″ ″ CCTGAAAAATC TGCAGAATTAAG CYP24  87 J14 plate 96 ET4211 104 C10 plate 754 ET03.17 121 C10 plate 10 D20S902 166 I4 plate 226 180-R 188 G21 plate F1/B1 163 164- 197 N13 plate 1Ff1/b2 309

cDNA Sequences from the 20q13 Amplicon.

Exon trapping (see, e.g., Duyk et al., Proc. Natl. Acad. Sci. USA, 87: 8995-8999 (1990) and Church et al., Nature Genetics, 6: 98-105 (1994)) was performed on the P1 and BAC clones spanning the ≈600 kb minimum common region of amplification and has isolated more than 200 exons.

Analysis of the exons DNA sequence revealed a number of sequence similarities (85% to 96%) to partial cDNA sequences in the expressed sequence data base (dbest) and to a S. cerevisiae chromosome XIV open reading frame. Each P1 clone subjected to exon trapping has produced multiple exons consistent with at least a medium density of genes. Over 200 exons have been trapped and analyzed as well as 200 clones isolated by direct selection from a BT474 cDNA library. In addition a 0.6 Mb genomic interval spanning the minimal amplicon described below is being sequenced. Exon prediction and gene modeling are carried out with XGRAIL, SORFIND, and BLAST programs. Gene fragments identified by these approaches have been analyzed by RT-PCR, Northern and Southern blots. Fifteen unique genes were identified in this way (see, Table 3 and FIG. 5).

In addition two other genes ZABC1 (SEQ. ID. 9 and 10) and 1b1 (SEQ ID No. 12) were also were shown to be overexpressed in a variety of different cancer cells.

Sequence information from various cDNA clones are provided below. They are as follows:

3bf4 (SEQ. ID. No. 1)—3 kb transcript with sequence identity to a tyrosine kinase gene, termed A6, disclosed in Beeler et al. Mol. Cell. Biol. 14:982-988 (1994) and WO 95/19439. These references, however, do not disclose that the gene is located in the chromosome 20 amplicon.

1b11 (SEQ. ID. No. 2)—an approximately 3.5 kb transcript whose expression shows high correlation with the copy number of the amplicon. The sequence shows no homology with sequences in the databases searched.

cc49 (SEQ. ID. No. 3)—a 6-7 kb transcript which shows homology to C2H2 zinc finger genes.

cc43 (SEQ. ID. No. 4)—an approximately 4 kb transcript which is expressed in normal tissues, but whose expression in the breast cancer cell line has not been detected.

41.1 (SEQ. ID. No. 5)—shows homology to the homeobox T shirt gene in Drosophila.

GCAP (SEQ. ID. No. 6)—encodes a guanino cyclase activating protein which is involved in the biosynthesis of cyclic AMP. As explained in detail below, sequences from this gene can also be used for treatment of retinal degeneration.

1b4 (SEQ. ID. No. 7)—a serine threonine kinase.

20sa7 (SEQ. ID. No. 8)—a homolog of the rat gene, BEM-1.

In addition, the entire nucleotide sequence is provided for ZABC-1. ZABC-1 stands for zinc finger amplified in breast cancer. This gene maps to the core of the 20q13.2 amplicon and is overexpressed in primary tumors and breast cancer cell lines having 20q13.2 amplification. The genomic sequence (SEQ. ID. No. 9) includes roughly 2kb of the promoter region. SEQ ID. No. 10 provides the cDNA sequence derived open reading frame and SEQ ID. No. 11 provides the predicted protein sequence. Zinc finger containing genes are often transcription factors that function to modulate the expression of down stream genes. Several known oncogenes are in fact zinc finger containing genes.

This invention also provides the full length cDNA sequence for a cDNA designated 1b1 (SEQ. ID. No. 12) which is also overexpressed in numerous breast cancer cell lines and some primary tumors.

SEQ ID NO: 13 provides sequence from a genomic clone which is similar to known rat and mouse cyclophilin cDNAs. Rat Cyclophilin nucleic acids (e.g., cDNAs) are known; see, GenBank™ under accession No. M19533; Mouse Cyclophilin nucleic acids (e.g., cDNAs) are known; see, GenBank™ under accession No. 50620 (see, FIG. 6). Accordingly, SEQ ID NO: 13 is a putative human cyclophilin gene. The sequence is also associated with amplified sequences from 20q13, and can be used as a probe or probe hybridization target to detect DNA amplification, or RNA overexpression of the corresponding gene.

TABLE 3 Gene fragments identified by exon trapping and analyzed by RT-PCR, Northern and Southern blots. EST Cloned Map Gene Transcript Identity Sequence Protein Map # ID Size (kb) (>95%) (kb) Homologies Location  1 20sa7 — Yes 3 PTP 3, 18, 99  2 1b11 3.5 No 1.5 novel 18, 3, 99, 69  3 200.1 — — — — —  4 132.1 — — — novel 132  5 132.2 — — — — 132  6 3bf4 3 Yes 3 PTK ambiguous  7 7.1 — — — — 7, 11, 97  8 7.2 2.4 — — — 7, 11, 97  9 cc49 7, 4 Yes 3.6 Kruppel 97, 103 10 cc43 1.4 Yes 1.8 hypothetical 97, 7, 11 yeast protein 11 et1807 2.5 Yes 0.7 novel 97, 9 12 et2106 None Yes — — 95, 39, 38 13 41.1 detected Yes 3 homeotic 95, 41, 42 14 67.1 7, 8, 11 Yes 2 Kb gene 67 15 67.2 — Yes — cGMP reg. 67 0 protein

20q13 Amplicon Proteins

As indicated above, this invention also provides for proteins encoded by nucleic acid sequences in the 20q13 amplicon (e.g., SEQ. ID. Nos: 1-10 and 12-13) and subsequences more preferably subsequences of at least 10 amino acids, preferably of at least 20 amino acids, and most preferably of at least 30 amino acids in length. Particularly referred subsequences are epitopes specific to the 20q13 proteins more preferably epitopes specific to the ZABC1 and 1b1 proteins. Such proteins include, but are not limited to isolated polypeptides comprising at least 10 contiguous amino acids from a polypeptide encoded by the nucleic acids of SEQ. ID No. 1-10 and 12-13 or from the polypeptide of SEQ. ID. No. 11 wherein the polypeptide, when presented as an immunogen, elicits the production of an antibody which specifically binds to a polypeptide selected from the group consisting of a polypeptide encoded by the nucleic acids of SEQ. ID No. 1-10 and 12-13 or from the polypeptide of SEQ. ID. No. 11 and the polypeptide does not bind to antisera raised against a polypeptide selected from the group consisting of a polypeptide encoded by the nucleic acids of SEQ. ID No. 1-10 and 12 or from the polypeptide of SEQ. ID. No. 11 which has been fully immunosorbed with a polypeptide selected from the group consisting of a polypeptide encoded by the nucleic acids of SEQ. ID No. 1-10 and 12-13 or from the polypeptide of SEQ. ID. No. 11.

A protein that specifically binds to or that is specifically immunoreactive with an antibody generated against a defined immunogen, such as an immunogen consisting of the amino acid sequence of SEQ ID NO 11 is determined in an immunoassay. The immunoassay uses a polyclonal antiserum which was raised to the protein of SEQ ID NO 11 (the immunogenic polypeptide). This antiserum is selected to have low cross reactivity against other similar known polypeptides and any such cross reactivity is removed by immunoabsorbtion prior to use in the immunoassay (e.g., by immunosorbtion of the antisera with the related polypeptide).

In order to produce antisera for use in an immunoassay, the polypeptide e.g., the polypeptide of SEQ ID NO 11 is isolated as described herein. For example, recombinant protein can be produced in a mammalian or other eukaryotic cell line. An inbred strain of mice is immunized with the protein of SEQ ID NO 11 using a standard adjuvant, such as Freund's adjuvant, and a standard mouse immunization protocol (see Harlow and Lane, supra). Alternatively, a synthetic polypeptide derived from the sequences disclosed herein and conjugated to a carrier protein is used as an immunogen. Polyclonal sera are collected and titered against the immunogenic polypeptide in an immunoassay, for example, a solid phase immunoassay with the immunogen immobilized on a solid support. Polyclonal antisera with a titer of 10⁴ or greater are selected and tested for their cross reactivity against known polypeptides using a competitive binding immunoassay such as the one described in Harlow and Lane, supra, at pages 570-573. Preferably more than one known polypeptide is used in this determination in conjunction with the immunogenic polypeptide.

The known polypeptides can be produced as recombinant proteins and isolated using standard molecular biology and protein chemistry techniques as described herein.

Immunoassays in the competitive binding format are used for cross reactivity determinations. For example, the immunogenic polypeptide is immobilized to a solid support. Proteins added to the assay compete with the binding of the antisera to the immobilized antigen. The ability of the a proteins to compete with the binding of the antisera to the immobilized protein is compared to the immunogenic polypeptide. The percent cross reactivity for the protein is calculated, using standard calculations. Those antisera with less than 10% cross reactivity to known polypeptides are selected and pooled. The cross-reacting antibodies are then removed from the pooled antisera by immunoabsorbtion with known polypeptide.

The immunoabsorbed and pooled antisera are then used in a competitive binding immunoassay as described herein to compare a “target” polypeptide to the immunogenic polypeptide. To make this comparison, the two polypeptides are each assayed at a wide range of concentrations and the amount of each polypeptide required to inhibit 50% of the binding of the antisera to the immobilized protein is determined using standard techniques. If the amount of the target polypeptide required is less than twice the amount of the immunogenic polypeptide that is required, then the target polypeptide is said to specifically bind to an antibody generated to the immunogenic protein. As a final determination of specificity, the pooled antisera is fully immunosorbed with the immunogenic polypeptide until no binding to the polypeptide used in the immunosorbtion is detectable. The fully immunosorbed antisera is then tested for reactivity with the test polypeptide. If no reactivity is observed, then the test polypeptide is specifically bound by the antisera elicited by the immunogenic protein.

Similarly, in a reciprocal experiment, the pooled antisera is immunosorbed with the test polypeptide. If the antisera which remains after the immunosorbtion does not bind to the immunogenic polypeptide (i.e., the polypeptide of SEQ ID NO: 11 used to elicit the antisera) then the test polypeptide is specifically bound by the antisera elicited by the immunogenic peptide.

Detection of 20q13 Abnormalities.

One of skill in the art will appreciate that the clones and sequence information provided herein can be used to detect amplifications, or other chromosomal abnormalities, at 20q13 in a biological sample. Generally the methods involve hybridization of probes that specifically bind one or more nucleic acid sequences of the target amplicon with nucleic acids present in a biological sample or derived from a biological sample.

As used herein, a biological sample is a sample of biological tissue or fluid containing cells desired to be sensed for chromosomal abnormalities (e.g. amplifications of deletions). In a preferred embodiment, the biological sample is a cell or tissue suspected of being cancerous (transformed). Methods of isolating biological samples are well known to those of skill in the art and include, but are not limited to, aspirations, tissue sections, needle biopsies, and the like. Frequently the sample will be a “clinical sample” which is a sample derived from a patient. It will be recognized that the term “sample” also includes supernatant (containing cells) or the cells themselves from cell cultures, cells from tissue culture and other media in which it may be desirable to detect chromosomal abnormalities.

In some embodiments, a chromosome sample is prepared by depositing cells, either as single cell suspensions or as tissue preparation, on solid supports such as glass slides and fixed by choosing a fixative which provides the best spatial resolution of the cells and the optimal hybridization efficiency. In other embodiments, the sample is contacted with an array of probes immobilized on a solid surface.

Making Probes

Any of the P1 probes listed in Table 1, the BAC probes listed in Table 2, or the cDNAs disclosed here are suitable for use in detecting the 20q13 amplicon. Methods of preparing probes are well known to those of skill in the art (see, e.g. Sambrook et al., Molecular Cloning: A Laboratory Manual (2nd ed.), Vols. 1-3, Cold Spring Harbor Laboratory, (1989) or Current Protocols in Molecular Biology, F. Ausubel et al., ed. Greene Publishing and Wiley-Interscience, New York (1987))

Given the strategy for making the nucleic acids of the present invention, one of skill can construct a variety of vectors and nucleic acid clones containing functionally equivalent nucleic acids. Cloning methodologies to accomplish these ends, and sequencing methods to verify the sequence of nucleic acids are well known in the art. Examples of appropriate cloning and sequencing techniques, and instructions sufficient to direct persons of skill through many cloning exercises are found in Berger and Kimmel, Guide to Molecular Cloning Techniques, Methods in Enzymology volume 152 Academic Press, Inc., San Diego, Calif. (Berger); Sambrook et al. (1989) Molecular Cloning—A Laboratory Manual (2nd ed.) Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor Press, NY, (Sambrook); and Current Protocols in Molecular Biology, F. M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (1994 Supplement) (Ausubel). Product information from manufacturers of biological reagents and experimental equipment also provide information useful in known biological methods. Such manufacturers include the SIGMA chemical company (Saint Louis, Mo.), R&D systems (Minneapolis, Minn.), Pharmacia LKB Biotechnology (Piscataway, N.J.), CLONTECH Laboratories, Inc. (Palo Alto, Calif.), Chem Genes Corp., Aldrich Chemical Company (Milwaukee, Wis.), Glen Research, Inc., GIBCO BRL Life Technologies, Inc. (Gaithersberg, Md.), Fluka Chemica-Biochemika Analytika (Fluka Chemie AG, Buchs, Switzerland), Invitrogen, San Diego, Calif., and Applied Biosystems (Foster City, Calif.), as well as many other commercial sources known to one of skill.

The nucleic acids provided by this invention, whether RNA, cDNA, genomic DNA, or a hybrid of the various combinations, are isolated from biological sources or synthesized in vitro. The nucleic acids and vectors of the invention are present in transformed or transfected whole cells, in transformed or transfected cell lysates, or in a partially purified or substantially pure form.

In vitro amplification techniques suitable for amplifying sequences to provide a nucleic acid, or for subsequent analysis, sequencing or subcloning are known. Examples of techniques sufficient to direct persons of skill through such in vitro amplification methods, including the polymerase chain reaction (PCR) the ligase chain reaction (LCR), Qβ-replicase amplification and other RNA polymerase mediated techniques (e.g., NASBA) are found in Berger, Sambrook, and Ausubel, as well as Mullis et al., (1987) U.S. Pat. No. 4,683,202; PCR Protocols A Guide to Methods and Applications (Innis et al. eds) Academic Press. Inc. San Diego, Calif. (1990) (Innis); Arnheim & Levinson (Oct. 1, 1990) C&EN 36-47; The Journal of NIH Research (1991) 3, 81-94; Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA 86, 1173; Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87, 1874; Lomell et al. (1989) J. Clin. Chem 35, 1826; Landegren et al., (1988) Science 241, 1077-1080; Van Brunt (1990) Biotechnology 8, 291-294; Wu and Wallace, (1989) Gene 4, 560; Barringer et al. (1990) Gene 89, 117, and Sooknanan and Malek (1995) Biotechnology 13: 563-564. Improved methods of cloning in vitro amplified nucleic acids are described in Wallace et al., U.S. Pat. No. 5,426,039. Improved methods of amplifying large nucleic acids are summarized in Cheng et al. (1994) Nature 369: 684-685 and the references therein.

Nucleic Acids (e.g., oligonucleotides) for in vitro amplification methods or for use as gene probes, for example, are typically chemically synthesized according to the solid phase phosphoramidite triester method described by Beaucage and Caruthers (1981), Tetrahedron Letts., 22(20):1859-1862, e.g., using an automated synthesizer, as described in Needham-VanDevanter et al. (1984) Nucleic Acids Res., 12:6159-6168. Purification of oligonucleotides, where necessary, is typically performed by either native acrylamide gel electrophoresis or by anion-exchange HPLC as described in Pearson and Regnier (1983) J. Chrom. 255:137-149. The sequence of the synthetic oligonucleotides can be verified using the chemical degradation method of Maxam and Gilbert (1980) in Grossman and Moldave (eds.) Academic Press, New York, Methods in Enzymology 65:499-560.

The probes are most easily prepared by combining and labeling one or more of the constructs listed in Tables 1 and 2. Prior to use, the constructs are fragmented to provide smaller nucleic acid fragments that easily penetrate the cell and hybridize to the target nucleic acid. Fragmentation can be by any of a number of methods well known to those of skill in the art. Preferred methods include treatment with a restriction enzyme to selectively cleave the molecules, or alternatively to briefly heat the nucleic acids in the presence of Mg²⁺. Probes are preferably fragmented to an average fragment length ranging from about 50 bp to about 2000 bp, more preferably from about 100 bp to about 1000 bp and most preferably from about 150 bp to about 500 bp.

Alternatively, probes can be produced by amplifying (e.g. via PCR) selected subsequences from the 20q13 amplicon disclosed herein. The sequences provided herein permit one of skill to select primers that amplify sequences from one or more exons located within the 20q13 amplicon.

Particularly preferred probes include nucleic acids from probes 38, 40, and 79, which corresponds to RMC20C001. In addition, the cDNAs are particularly useful for identifying cells that have increased expression of the corresponding genes, using for instance, Northern blot analysis.

One of skill will appreciate that using the sequence information and clones provided herein, one of skill in the art can isolate the same or similar probes from other human genomic libraries using routine methods (e.g. Southern or Northern Blots).

Similarly, the polypeptides of the invention can be synthetically prepared in a wide variety of well-know ways. For instance, polypeptides of relatively short length can be synthesized in solution or on a solid support in accordance with conventional techniques. See, e.g., Merrifield (1963) J. Am. Chem. Soc. 85:2149-2154. Various automatic synthesizers are commercially available and can be used in accordance with known protocols. See, e.g., Stewart and Young (1984) Solid Phase Peptide Synthesis, 2d. ed., Pierce Chemical Co. As described in more detail herein, the polypeptide of the invention are most preferably made using recombinant techniques, e.g., by expressing the polypeptides in host cells and purifying the expressed proteins.

In a preferred embodiment, the polypeptides, or subsequences thereof, are synthesized using recombinant DNA methodology. Generally this involves creating a DNA sequence that encodes the protein, through recombinant, synthetic, or in vitro amplification techniques, placing the DNA in an expression cassette under the control of a particular promoter, expressing the protein in a host cell, isolating the expressed protein and, if required, renaturing the protein.

Labeling Nucleic Acids

Methods of labeling nucleic acids (either probes or sample nucleic acids) are well known to those of skill in the art. Preferred labeled labels are those that are suitable for use in in situ hybridization. The nucleic acid probes or samples of the invention may be detectably labeled prior to the hybridization reaction. Alternatively, a detectable label which binds to the hybridization product may be used. Such detectable labels include any material having a detectable physical or chemical property and have been well-developed in the field of immunoassays.

As used herein, a “label” is any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means. Useful labels in the present invention include radioactive labels (e.g. ³²P, ¹²⁵I, ¹⁴C, ³H, and ³⁵S), fluorescent dyes (e.g. fluorescein, rhodamine, Texas Red, etc.), electron-dense reagents (e.g. gold), enzymes (as commonly used in an ELISA), calorimetric labels (e.g. colloidal gold), magnetic labels (e.g. Dynabeads™), and the like. Examples of labels which are not directly detected but are detected through the use of directly detectable label include biotin and dioxigenin as well as haptens and proteins for which labeled antisera or monoclonal antibodies are available.

The particular label used is not critical to the present invention, so long as it does not interfere with the in situ hybridization of the stain. However, stains directly labeled with fluorescent labels (e.g. fluorescein-12-dUTP, Texas Red-5-dUTP, etc.) are preferred for chromosome hybridization.

A direct labeled probe, as used herein, is a probe to which a detectable label is attached. Because the direct label is already attached to the probe, no subsequent steps are required to associate the probe with the detectable label. In contrast, an indirect labeled probe is one which bears a moiety to which a detectable label is subsequently bound, typically after the probe is hybridized with the target nucleic acid.

In addition the label must be detectable in as low copy number as possible thereby maximizing the sensitivity of the assay and yet be detectable above any background signal. Finally, a label must be chosen that provides a highly localized signal thereby providing a high degree of spatial resolution when physically mapping the stain against the chromosome. Particularly preferred fluorescent labels include fluorescein-12-dUTP and Texas Red-5-dUTP.

The labels may be coupled to the probes in a variety of means known to those of skill in the art. In a preferred embodiment the nucleic acid probes will be labeled using nick translation or random primer extension (Rigby, et al. J. Mol. Biol., 113: 237 (1977) or Sambrook, et al., Molecular Cloning—A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1985)).

One of skill in the art will appreciate that the probes of this invention need not be absolutely specific for the targeted 20q13 region of the genome. Rather, the probes are intended to produce “staining contrast”. “Contrast” is quantified by the ratio of the probe intensity of the target region of the genome to that of the other portions of the genome. For example, a DNA library produced by cloning a particular chromosome (e.g. chromosome 7) can be used as a stain capable of staining the entire chromosome. The library contains both sequences found only on that chromosome, and sequences shared with other chromosomes. Roughly half the chromosomal DNA falls into each class. If hybridization of the whole library were capable of saturating all of the binding sites on the target chromosome, the target chromosome would be twice as bright (contrast ratio of 2) as the other chromosomes since it would contain signal from the both the specific and the shared sequences in the stain, whereas the other chromosomes would only be stained by the shared sequences. Thus, only a modest decrease in hybridization of the shared sequences in the stain would substantially enhance the contrast. Thus contaminating sequences which only hybridize to non-targeted sequences, for example, impurities in a library, can be tolerated in the stain to the extent that the sequences do not reduce the staining contrast below useful levels.

Detecting the 20q13 Amplicon.

As explained above, detection of amplification in the 20q13 amplicon is indicative of the presence and/or prognosis of a large number of cancers. These include, but are not limited to breast, ovary, bladder, head and neck, and colon.

In a preferred embodiment, a 20q13 amplification is detected through the hybridization of a probe of this invention to a target nucleic acid (e.g. a chromosomal sample) in which it is desired to screen for the amplification. Suitable hybridization formats are well known to those of skill in the art and include, but are not limited to, variations of Southern Blots, in situ hybridization and quantitative amplification methods such as quantitative PCR (see, e.g. Sambrook, supra., Kallioniemi et al., Proc. Natl Acad Sci USA, 89: 5321-5325 (1992), and PCR Protocols, A Guide to Methods and Applications, Innis et al., Academic Press, Inc. N.Y., (1990)).

In situ Hybridization.

In a preferred embodiment, the 20q13 amplicon is identified using in situ hybridization. Generally, in situ hybridization comprises the following major steps: (1) fixation of tissue or biological structure to analyzed; (2) prehybridization treatment of the biological structure to increase accessibility of target DNA, and to reduce nonspecific binding; (3) hybridization of the mixture of nucleic acids to the nucleic acid in the biological structure or tissue; (4) posthybridization washes to remove nucleic acid fragments not bound in the hybridization and (5) detection of the hybridized nucleic acid fragments. The reagent used in each of these steps and their conditions for use vary depending on the particular application.

In some applications it is necessary to block the hybridization capacity of repetitive sequences. In this case, human genomic DNA is used as an agent to block such hybridization. The preferred size range is from about 200 bp to about 1000 bases, more preferably between about 400 to about 800 bp for double stranded, nick translated nucleic acids.

Hybridization protocols for the particular applications disclosed here are described in Pinkel et al. Proc. Natl. Acad. Sci. USA, 85: 9138-9142 (1988) and in EPO Pub. No. 430,402. Suitable hybridization protocols can also be found in Methods o\in Molecular Biology Vol. 33: In Situ Hybridization Protocols, K. H. A. Choo, ed., Humana Press, Totowa, N.J., (1994). In a particularly preferred embodiment, the hybridization protocol of Kallioniemi et al., Proc. Natl Acad Sci USA, 89: 5321-5325 (1992) is used.

Typically, it is desirable to use dual color FISH, in which two probes are utilized, each labeled by a different fluorescent dye. A test probe that hybridizes to the region of interest is labeled with one dye, and a control probe that hybridizes to a different region is labeled with a second dye. A nucleic acid that hybridizes to a stable portion of the chromosome of interest, such as the centromere region, is often most useful as the control probe. In this way, differences between efficiency of hybridization from sample to sample can be accounted for.

The FISH methods for detecting chromosomal abnormalities can be performed on nanogram quantities of the subject nucleic acids. Paraffin embedded tumor sections can be used, as can fresh or frozen material. Because FISH can be applied to the limited material, touch preparations prepared from uncultured primary tumors can also be used (see, e.g., Kallioniemi, A. et al., Cytogenet. Cell Genet. 60: 190-193 (1992)). For instance, small biopsy tissue samples from tumors can be used for touch preparations (see, e.g., Kallioniemi, A. et al., Cytogenet. Cell Genet. 60: 190-193 (1992)). Small numbers of cells obtained from aspiration biopsy or cells in bodily fluids (e.g., blood, urine, sputum and the like) can also be analyzed. For prenatal diagnosis, appropriate samples will include amniotic fluid and the like.

Other Formats

A number of hybridization formats are useful in the invention. For instance, Southern hybridizations can be used. In a Southern Blot, a genomic or cDNA (typically fragmented and separated on an electrophoretic gel) is hybridized to a probe specific for the target region. Comparison of the intensity of the hybridization signal from the probe for the target region (e.g., 20q13) with the signal from a probe directed to a control (non amplified) such as centromeric DNA, provides an estimate of the relative copy number of the target nucleic acid.

Other formats use arrays of probes or targets to which nucleic acid samples are hybridized as described, for instance, in WO 96/17958. As used herein, a “nucleic acid array” is a plurality of target elements, each comprising one or more target nucleic acid molecules immobilized on a solid surface to which probe nucleic acids are hybridized. Target nucleic acids of a target element typically have their origin in the 20q13 amplicon. The target nucleic acids of a target element may, for example, contain sequence from specific genes or clones disclosed here. Target elements of various dimensions can be used in the arrays of the invention. Generally, smaller, target elements are preferred. Typically, a target element will be less than about 1 cm in diameter. Generally element sizes are from 1 μm to about 3 mm, preferably between about 5 μm and about 1 mm.

The target elements of the arrays may be arranged on the solid surface at different densities. The target element densities will depend upon a number of factors, such as the nature of the label, the solid support, and the like. One of skill will recognize that each target element may comprise a mixture of target nucleic acids of different lengths and sequences. Thus, for example, a target element may contain more than one copy of a cloned piece of DNA, and each copy may be broken into fragments of different lengths. The length and complexity of the target sequences of the invention is not critical to the invention. One of skill can adjust these factors to provide optimum hybridization and signal production for a given hybridization procedure, and to provide the required resolution among different genes or genomic locations. Typically, the target sequences will have a complexity between about 1 kb and about 1 Mb, sometimes 10 kb and about 500 kb, and usually from about 50 kb to about 150 kb.

Detecting Mutations in Genes from the 20q13 Amplicon

The cDNA sequences disclosed here can also be used for detecting mutations (e.g., substitutions, insertions, and deletions) within the corresponding endogenous genes. One of skill will recognize that the nucleic acid hybridization techniques generally described above can be adapted to detect such much mutations. For instance, oligonucleotide probes that distinguish between mutant and wild-type forms of the target gene can be used in standard hybridization assays. In some embodiments, amplification (e.g., using PCR) can be used to increase copy number of the target sequence prior to hybridization.

Assays for Detecting 20q13 Amplicon Proteins.

As indicated above, this invention identifies protein products of genes in the 20q13 amplicon that are associated with various cancers. In particular, it was shown that 20q13 proteins were overexpressed in various cancers. The presence or absence and/or level of expression of 20q13 proteins can be indicative of the presence, absence, or extent of a cancer. Thus, 20q13 proteins can provide useful diagnostic markers.

The 20q13 amplicon proteins (e.g., ZABC1 or 1b1) can be detected and quantified by any of a number of means well known to those of skill in the art. These may include analytic biochemical methods such as electrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), hyperdiffusion chromatography, and the like, or various immunological methods such as fluid or gel precipitin reactions, immunodiffusion (single or double), immunoelectrophoresis, radioimmunoassay(RIA), enzyme-linked immunosorbent assays (ELISAs), immunofluorescent assays, western blotting, and the like.

In one preferred embodiment, the 20q13 amplicon proteins are detected in an electrophoretic protein separation such as a one dimensional or two-dimensional electrophoresis, while in a most preferred embodiment, the 20q13 amplicon proteins are detected using an immunoassay.

As used herein, an immunoassay is an assay that utilizes an antibody to specifically bind to the analyte (e.g., ZABC1 or 1b1 proteins). The immunoassay is thus characterized by detection of specific binding of a 20q13 amplicon protein to an anti-20q13 amplicon antibody (e.g., anti-ZABC1 or anti-1b1) as opposed to the use of other physical or chemical properties to isolate, target, and quantify the analyte.

The collection of biological sample and subsequent testing for 20q13 amplicon protein(s) is discussed in more detail below.

A) Sample Collection and Processing

The 20q13 amplicon proteins are preferably quantified in a biological sample derived from a mammal, more preferably from a human patient or from a porcine, murine, feline, canine, or bovine. As used herein, a biological sample is a sample of biological tissue or fluid that contains a 20q13 amplicon protein concentration that may be correlated with a 20q13 amplification. Particularly preferred biological samples include, but are not limited to biological fluids such as blood or urine, or tissue samples including, but not limited to tissue biopsy (e.g., needle biopsy) samples.

The biological sample may be pretreated as necessary by dilution in an appropriate buffer solution or concentrated, if desired. Any of a number of standard aqueous buffer solutions, employing one of a variety of buffers, such as phosphate, Tris, or the like, at physiological pH can be used.

B) Electrophoretic Assays

As indicated above, the presence or absence of 20q13 amplicon proteins in a biological tissue may be determined using electrophoretic methods. Means of detecting proteins using electrophoretic techniques are well known to those of skill in the art (see generally, R. Scopes (1982) Protein Purification, Springer-Verlag, N.Y.; Deutscher, (1990) Methods in Enymology Vol. 182: Guide to Protein Purification, Academic Press, Inc., N.Y.). In a preferred embodiment, the 20q13 amplicon proteins are detected using one-dimensional or two-dimensional electrophoresis. A particularly preferred two-dimensional electrophoresis separation relies on isoelectric focusing (IEF) in immobilized pH gradients for one dimension and polyacrylamide gels for the second dimension. Such assays are described in the cited references and by Patton et al. (1990) Biotechniques 8: 518.

C) Immunological Binding Assays.

In a preferred embodiment, the 20q13 amplicon are detected and/or quantified using any of a number of well recognized immunological binding assays (see, e.g., U.S. Pat. Nos. 4,366,241; 4,376,110; 4,517,288; and 4,837,168). For a review of the general immunoassays, see also Methods in Cell Biology Volume 37: Antibodies in Cell Biology, Asai, ed. Academic Press, Inc. New York (1993); Basic and Clinical Immunology 7th Edition, Stites & Terr, eds. (1991).

Immunological binding assays (or immunoassays) typically utilize a “capture agent” to specifically bind to and often immobilize the analyte (in this case 20q13 amplicon). The capture agent is a moiety that specifically binds to the analyte. In a preferred embodiment, the capture agent is an antibody that specifically binds 20q13 amplicon protein(s).

The antibody (e.g., anti-ZABC1 or anti-1b1) may be produced by any of a number of means well known to those of skill in the art (see, e.g. Methods in Cell Biology Volume 37: Antibodies in Cell Biology, Asai, ed. Academic Press, Inc. New York (1993); and Basic and Clinical Immunology 7th Edition, Stites & Terr, eds. (1991)). The antibody may be a whole antibody or an antibody fragment. It may be polyclonal or monoclonal, and it may be produced by challenging an organism (e.g. mouse, rat, rabbit, etc.) with a 20q13 amplicon protein or an epitope derived therefrom. Alternatively, the antibody may be produced de novo using recombinant DNA methodology. The antibody can also be selected from a phage display library screened against 20q13 amplicon (see, e.g. Vaughan et al. (1996) Nature Biotechnology, 14: 309-314 and references therein).

Immunoassays also often utilize a labeling agent to specifically bind to and label the binding complex formed by the capture agent and the analyte. The labeling agent may itself be one of the moieties comprising the antibody/analyte complex. Thus, the labeling agent may be a labeled 20q13 amplicon protein or a labeled anti-20q13 amplicon antibody. Alternatively, the labeling agent may be a third moiety, such as another antibody, that specifically binds to the antibody/20q13 amplicon protein complex.

In a preferred embodiment, the labeling agent is a second human 20q13 amplicon protein antibody bearing a label. Alternatively, the second 20q13 amplicon protein antibody may lack a label, but it may, in turn, be bound by a labeled third antibody specific to antibodies of the species from which the second antibody is derived. The second can be modified with a detectable moiety, such as biotin, to which a third labeled molecule can specifically bind, such as enzyme-labeled streptavidin.

Other proteins capable of specifically binding immunoglobulin constant regions, such as protein A or protein G may also be used as the label agent. These proteins are normal constituents of the cell walls of streptococcal bacteria. They exhibit a strong non-immunogenic reactivity with immunoglobulin constant regions from a variety of species. See, generally Kronval, et al., J. Immunol., 111:1401-1406 (1973), and Akerstrom, et al., J. Immunol., 135:2589-2542 (1985).

Throughout the assays, incubation and/or washing steps may be required after each combination of reagents. Incubation steps can vary from about 5 seconds to several hours, preferably from about 5 minutes to about 24 hours. However, the incubation time will depend upon the assay format, analyte, volume of solution, concentrations, and the like. Usually, the assays will be carried out at ambient temperature, although they can be conducted over a range of temperatures, such as 10° C. to 40° C.

1) Non-Competitive Assay Formats.

Immunoassays for detecting 20q13 amplicon proteins may be either competitive or noncompetitive. Noncompetitive immunoassays are assays in which the amount of captured analyte (in this case. 20q13 amplicon) is directly measured. In one preferred “sandwich” assay, for example, the capture agent (anti-20q13 amplicon protein antibodies) can be bound directly to a solid substrate where they are immobilized. These immobilzed antibodies then capture 20q13 amplicon protein present in the test sample. The 20q13 amplicon protein thus immobilized is then bound by a labeling agent, such as a second human 20q13 amplicon protein antibody bearing a label. Alternatively, the second 20q13 amplicon protein antibody may lack a label, but it may, in turn, be bound by a labeled third antibody specific to antibodies of the species from which the second antibody is derived. The second can be modified with a detectable moiety, such as biotin, to which a third labeled molecule can specifically bind, such as enzyme-labeled streptavidin.

2. Competitive Assay Formats.

In competitive assays, the amount of analyte (20q13 amplicon protein) present in the sample is measured indirectly by measuring the amount of an added (exogenous) analyte (20q13 amplicon proteins such as ZABC1 or 1b1 protein) displaced (or competed away) from a capture agent (e.g., anti-ZABC1 or anti-1b1 antibody) by the analyte present in the sample. In one competitive assay, a known amount of, in this case, 20q13 amplicon protein is added to the sample and the sample is then contacted with a capture agent, in this case an antibody that specifically binds 20q13 amplicon protein. The amount of 20q13 amplicon protein bound to the antibody is inversely proportional to the concentration of 20q13 amplicon protein present in the sample.

In a particularly preferred embodiment, the anti-20q13 protein antibody is immobilized on a solid substrate. The amount of 20q13 amplicon protein bound to the antibody may be determined either by measuring the amount of 20q13 amplicon present in an 20q13 amplicon protein/antibody complex, or alternatively by measuring the amount of remaining uncomplexed 20q13 amplicon protein. The amount of 20q13 amplicon protein may be detected by providing a labeled 20q13 amplicon protein.

A hapten inhibition assay is another preferred competitive assay. In this assay a known analyte, in this case 20q13 amplicon protein is immobilized on a solid substrate. A known amount of anti-20q13 amplicon protein antibody is added to the sample, and the sample is then contacted with the immobilized 20q13 amplicon protein. In this case, the amount of anti-20q13 amplicon protein antibody bound to the immobilized 20q13 amplicon protein is inversely proportional to the amount of 20q13 amplicon protein present in the sample. Again the amount of immobilized antibody may be detected by detecting either the immobilized fraction of antibody or the fraction of the antibody that remains in solution. Detection may be direct where the antibody is labeled or indirect by the subsequent addition of a labeled moiety that specifically binds to the antibody as described above.

3. Other Assay Formats

In a particularly preferred embodiment, Western blot (immunoblot) analysis is used to detect and quantify the presence of 20q13 amplicon protein in the sample. The technique generally comprises separating sample proteins by gel electrophoresis on the basis of molecular weight, transferring the separated proteins to a suitable solid support, (such as a nitrocellulose filter, a nylon filter, or derivatized nylon filter), and incubating the sample with the antibodies that specifically bind 20q13 amplicon protein. The anti-20q13 amplicon protein antibodies specifically bind to 20q13 amplicon protein on the solid support. These antibodies may be directly labeled or alternatively may be subsequently detected using labeled antibodies (e.g., labeled sheep anti-mouse antibodies) that specifically bind to the anti-20q13 amplicon protein.

Other assay formats include liposome immunoassays (LIA), which use liposomes designed to bind specific molecules (e.g., antibodies) and release encapsulated reagents or markers. The released chemicals are then detected according to standard techniques (see, Monroe et al. (1986) Amer. Clin. Prod. Rev. 5:34-41).

D) Reduction of Non-Specific Binding

One of skill in the art will appreciate that it is often desirable to reduce non-specific binding in immunoassays. Particularly, where the assay involves an antigen or antibody immobilized on a solid substrate it is desirable to minimize the amount of non-specific binding to the substrate. Means of reducing such non-specific binding are well known to those of skill in the art. Typically, this involves coating the substrate with a proteinaceous composition. In particular, protein compositions such as bovine serum albumin (BSA), nonfat powdered milk, and gelatin are widely used with powdered milk being most preferred.

E) Labels

The particular label or detectable group used in the assay is not a critical aspect of the invention, so long as it does not significantly interfere with the specific binding of the antibody used in the assay. The detectable group can be any material having a detectable physical or chemical property. Such detectable labels have been well-developed in the field of immunoassays and, in general, most any label useful in such methods can be applied to the present invention. Thus, a label is any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Useful labels in the present invention include magnetic beads (e.g. Dynabeads™), fluorescent dyes (e.g., fluorescein isothiocyanate, texas red, rhodamine, and the like), radiolabels (e.g., ³H, ¹²⁵I, ³⁵S, ¹⁴C, or ³²P), enzymes (e.g., horse radish peroxidase, alkaline phosphatase and others commonly used in an ELISA), and colorimetric labels such as colloidal gold or colored glass or plastic (e.g. polystyrene, polypropylene, latex, etc.) beads.

The label may be coupled directly or indirectly to the desired component of the assay according to methods well known in the art. As indicated above, a wide variety of labels may be used, with the choice of label depending on sensitivity required, ease of conjugation with the compound, stability requirements, available instrumentation, and disposal provisions.

Non-radioactive labels are often attached by indirect means. Generally, a ligand molecule (e.g., biotin) is covalently bound to the molecule. The ligand then binds to an anti-ligand (e.g., streptavidin) molecule which is either inherently detectable or covalently bound to a signal system, such as a detectable enzyme, a fluorescent compound, or a chemilumineseent compound. A number of ligands and anti-ligands can be used. Where a ligand has a natural anti-ligand, for example, biotin, thyroxine, and cortisol, it can be used in conjunction with the labeled, naturally occurring anti-ligands. Alternatively, any haptenic or antigenic compound can be used in combination with an antibody.

The molecules can also be conjugated directly to signal generating compounds, e.g., by conjugation with an enzyme or fluorophore. Enzymes of interest as labels will primarily be hydrolases, particularly phosphatases, esterases and glycosidases, or oxidoreductases, particularly peroxidases. Fluorescent compounds include fluorescein and its derivatives, rhodamine and its derivatives, dansyl, umbelliferone, etc. Chemiluminescent compounds include luciferin, and 2,3-dihydrophthalazinediones, e.g., luminol. For a review of various labeling or signal producing systems which may be used, see, U.S. Pat. No. 4,391,904).

Means of detecting labels are well known to those of skill in the art. Thus, for example, where the label is a radioactive label, means for detection include a scintillation counter or photographic film as in autoradiography. Where the label is a fluorescent label, it may be detected by exciting the fluorochrome with the appropriate wavelength of light and detecting the resulting fluorescence. The fluorescence may be detected visually, by means of photographic film, by the use of electronic detectors such as charge coupled devices (CCDs) or photomultipliers and the like. Similarly, enzymatic labels may be detected by providing the appropriate substrates for the enzyme and detecting the resulting reaction product. Finally simple calorimetric labels may be detected simply by observing the color associated with the label. Thus, in various dipstick assays, conjugated gold often appears pink, while various conjugated beads appear the color of the bead.

Some assay formats do not require the use of labeled components. For instance, agglutination assays can be used to detect the presence of the target antibodies. In this case, antigen-coated particles are agglutinated by samples comprising the target antibodies. In this format, none of the components need be labeled and the presence of the target antibody is detected by simple visual inspection.

G) Substrates

As mentioned above, depending upon the assay, various components, including the antigen, target antibody, or anti-human antibody, may be bound to a solid surface. Many methods for immobilizing biomolecules to a variety of solid surfaces are known in the art. For instance, the solid surface may be a membrane (e.g., nitrocellulose), a microtiter dish (e.g., PVC, polypropylene, or polystyrene), a test tube (glass or plastic), a dipstick (e.g. glass, PVC, polypropylene, polystyrene, latex, and the like), a microcentrifuge tube, or a glass or plastic bead. The desired component may be covalently bound or noncovalently attached through nonspecific bonding.

A wide variety of organic and inorganic polymers, both natural and synthetic may be employed as the material for the solid surface. Illustrative polymers include polyethylene, polypropylene, poly(4-methylbutene), polystyrene, polymethacrylate, poly(ethylene terephthalate), rayon, nylon, poly(vinyl butyrate), polyvinylidene difluoride (PVDF), silicones, polyformaldehyde, cellulose, cellulose acetate, nitrocellulose, and the like. Other materials which may be employed, include paper, glasses, ceramics, metals, metalloids, semiconductive materials, cements or the like. In addition, are included substances that form gels, such as proteins (e.g., gelatins), lipopolysaccharides, silicates, agarose and polyacrylamides can be used. Polymers which form several aqueous phases, such as dextrans, polyalkylene glycols or surfactants, such as phospholipids, long chain (12-24 carbon atoms) alkyl ammonium salts and the like are also suitable. Where the solid surface is porous, various pore sizes may be employed depending upon the nature of the system.

In preparing the surface, a plurality of different materials may be employed, particularly as laminates, to obtain various properties. For example, protein coatings, such as gelatin can be used to avoid non-specific binding, simplify covalent conjugation, enhance signal detection or the like.

If covalent bonding between a compound and the surface is desired, the surface will usually be polyfunctional or be capable of being polyfunctionalized. Functional groups which may be present on the surface and used for linking can include carboxylic acids, aldehydes, amino groups, cyano groups, ethylenic groups, hydroxyl groups, mercapto groups and the like. The manner of linking a wide variety of compounds to various surfaces is well known and is amply illustrated in the literature. See, for example, Immobilized Enzymes, Ichiro Chibata, Halsted Press, New York, 1978, and Cuatrecasas (1970) J. Biol. Chem. 245 3059).

In addition to covalent bonding, various methods for noncovalently binding an assay component can be used. Noncovalent binding is typically nonspecific absorption of a compound to the surface. Typically, the surface is blocked with a second compound to prevent nonspecific binding of labeled assay components. Alternatively, the surface is designed such that it nonspecifically binds one component but does not significantly bind another. For example, a surface bearing a lectin such as Concanavalin A will bind a carbohydrate containing compound but not a labeled protein that lacks glycosylation. Various solid surfaces for use in noncovalent attachment of assay components are reviewed in U.S. Pat. Nos. 4,447,576 and 4,254,082.

Kits Containing 20q13 Amplicon Probes.

This invention also provides diagnostic kits for the detection of chromosomal abnormalities at 20q13. In a preferred embodiment, the kits include one or more probes to the 20q13 amplicon and/or antibodies to a 20q13 amplicon (e.g., anti-ZABC1 or anti-1b1) described herein. The kits can additionally include blocking probes, instructional materials describing how to use the kit contents in detecting 20q13 amplicons. The kits may also include one or more of the following: various labels or labeling agents to facilitate the detection of the probes, reagents for the hybridization including buffers, a metaphase spread, bovine serum albumin (BSA) and other blocking agents, sampling devices including fine needles, swabs, aspirators and the like, positive and negative hybridization controls and so forth.

Expression of cDNA Clones

One may express the desired polypeptides encoded by the cDNA clones disclosed here, or by subcloning cDNA portions of genomic sequences in a recombinantly engineered cell such as bacteria, yeast, insect (especially employing baculoviral vectors), or mammalian cell. It is expected that those of skill in the art are knowledgeable in the numerous expression systems available for expression of the cDNAs. No attempt to describe in detail the various methods known for the expression of proteins in prokaryotes or eukaryotes will be made.

In brief summary, the expression of natural or synthetic nucleic acids encoding polypeptides of the invention will typically be achieved by operably linking the DNA or cDNA to a promoter (which is either constitutive or inducible), followed by incorporation into an expression vector. The vectors can be suitable for replication and integration in either prokaryotes or eukaryotes. Typical expression vectors contain transcription and translation terminators, initiation sequences, and promoters useful for regulation of the expression of the DNA encoding the polypeptides. To obtain high level expression of a cloned gene, it is desirable to construct expression plasmids which contain, at the minimum, a strong promoter to direct transcription, a ribosome binding site for translational initiation, and a transcription/translation terminator.

Examples of regulatory regions suitable for this purpose in E. coli are the promoter and operator region of the E. coli tryptophan biosynthetic pathway as described by Yanofsky, C., 1984, J. Bacteriol., 158:1018-1024 and the leftward promoter of phage lambda (P_(L)) as described by Herskowitz, I. and Hagen, D., 1980, Ann. Rev. Genet., 14:399-445. The inclusion of selection markers in DNA vectors transformed in E. coli is also useful. Examples of such markers include genes specifying resistance to ampicillin, tetracycline, or chloramphenicol. Expression systems are available using E. coli, Bacillus sp. (Pava, I et al., 1983, Gene 22:229-235; Mosbach, K. et al. Nature, 302:543-545 and Salmonella. E. coli systems are preferred.

The polypeptides produced by prokaryote cells may not necessarily fold properly. During purification from E. coli, the expressed polypeptides may first be denatured and then renatured. This can be accomplished by solubilizing the bacterially produced proteins in a chaotropic agent such as guanidine HCl and reducing all the cysteine residues with a reducing agent such as beta-mercaptoethanol. The polypeptides are then renatured, either by slow dialysis or by gel filtration. U.S. Pat. No. 4,511,503.

A variety of eukaryotic expression systems such as yeast, insect cell lines and mammalian cells, are known to those of skill in the art. As explained briefly below, the polypeptides may also be expressed in these eukaryotic systems.

Synthesis of heterologous proteins in yeast is well known and described. Methods in Yeast Genetics, Sherman, F., et al., Cold Spring Harbor Laboratory, (1982) is a well recognized work describing the various methods available to produce the polypeptides in yeast. A number of yeast expression plasmids like YEp6, YEp13, YEp4 can be used as vectors. A gene of interest can be fused to any of the promoters in various yeast vectors. The above-mentioned plasmids have been fully described in the literature (Botstein, et al., 1979, Gene, 8:17-24; Broach, et al., 1979, Gene, 8:121-133).

Illustrative of cell cultures useful for the production of the polypeptides are cells of insect or mammalian origin. Mammalian cell systems often will be in the form of monolayers of cells although mammalian cell suspensions may also be used. Illustrative examples of mammalian cell lines include VERO and HeLa cells, Chinese hamster ovary (CHO) cell lines, W138, BHK, Cos-7 or MDCK cell lines.

As indicated above, the vector, e.g., a plasmid, which is used to transform the host cell, preferably contains DNA sequences to initiate transcription and sequences to control the translation of the antigen gene sequence. These sequences are referred to as expression control sequences. When the host cell is of insect or mammalian origin illustrative expression control sequences are often obtained from the SV-40 promoter (Science, 222:524-527, 1983), the CMV I.E. Promoter (Proc. Natl. Acad. Sci. 81:659-663, 1984) or the metallothionein promoter (Nature 296:39-42, 1982). The cloning vector containing the expression control sequences is cleaved using restriction enzymes and adjusted in size as necessary or desirable and ligated with the desired DNA by means well known in the art.

As with yeast, when higher animal host cells are employed, polyadenlyation or transcription terminator sequences from known mammalian genes need to be incorporated into the vector. An example of a terminator sequence is the polyadenlyation sequence from the bovine growth hormone gene. Sequences for accurate splicing of the transcript may also be included. An example of a splicing sequence is the VP1 intron from SV40 (Sprague, J. et al., 1983, J. Virol. 45: 773-781).

Additionally, gene sequences to control replication in the host cell may be incorporated into the vector such as those found in bovine papilloma virus type-vectors. Saveria-Campo, M., 1985, “Bovine Papilloma virus DNA a Eukaryotic Cloning Vector” in DNA Cloning Vol. II a Practical Approach Ed. D. M. Glover, IRL Press, Arlington, Va. pp. 213-238.

Therapeutic and Other uses of cDNAs and Their Gene Products

The cDNA sequences and the polypeptide products of the invention can be used to modulate the activity of the gene products of the endogenous genes corresponding to the cDNAs. By modulating activity of the gene products, pathological conditions associated with their expression or lack of expression can be treated. Any of a number of techniques well known to those of skill in the art can be used for this purpose.

The cDNAs of the invention are particularly used for the treatment of various cancers such as cancers of the breast, ovary, bladder, head and neck, and colon. Other diseases may also be treated with the sequences of the invention. For instance, as noted above, GCAP (SEQ. ID. No. 6) encodes a guanino cyclase activating protein which is involved in the biosynthesis of cyclic AMP. Mutations in genes involved in the biosynthesis of cyclic AMP are known to be associated with hereditary retinal degenerative diseases. These diseases are a group of inherited conditions in which progressive, bilateral degeneration of retinal structures leads to loss of retinal function. These diseases include age-related macular degeneration, a leading cause of visual impairment in the elderly; Leber's congenital amaurosis, which causes its victims to be born blind; and retinitis pigmentosa (“RP”), one of the most common forms of inherited blindness. RP is the name given to those inherited retinopathies which are characterized by loss of retinal photoreceptors (rods and cones), with retinal electrical responses to light flashes (i.e. eletroretinograms, or “ERGs”) that are reduced in amplitude.

The mechanism of retinal photoreceptor loss or cell death in different retinal degenerations is not fully understood. Mutations in a number of different genes have been identified as the primary genetic lesion in different forms of human RP. Affected genes include rhodopsin, the alpha and beta subunits of cGMP photodiesterase, and peripherin-RDS (Dryja, T. P. et al., Invest. Ophthalmol. Vis. Sci. 36, 1197-1200 (1995)). In all cases the manifestations of the disorder regardless of the specific primary genetic mutation is similar, resulting in photoreceptor cell degeneration and blindness.

Studies on animal models of retinal degeneration have been the focus of many laboratories during the last decade. The mechanisms that are altered in some of the mutations leading to blindness have been elucidated. This would include the inherited disorders of the rd mouse. The rd gene encodes the beta subunit of cGMP-phosphodiesterase (PDE) (Bowes, C. et al., Nature 347, 677-680 (1990)), an enzyme of fundamental importance in normal visual function because it is a key component in the cascade of events that takes place in phototransduction.

The polypeptides encoded by the cDNAs of the invention can be used as immunogens to raise antibodies either polyclonal or monoclonal. The antibodies can be used to detect the polypeptides for diagnostic purposes, as therapeutic agents to inhibit the polypeptides, or as targeting moieties in immunotoxins. The production of monoclonal antibodies against a desired antigen is well known to those of skill in the art and is not reviewed in detail here.

Those skilled in the art recognize that there are many methods for production and manipulation of various immunoglobulin molecules. As used herein, the terms “immunoglobulin” and “antibody” refer to a protein consisting of one or more polypeptides substantially encoded by immunoglobulin genes. Immunoglobulins may exist in a variety of forms besides antibodies, including for example, Fv, Fab, and F(ab)₂, as well as in single chains. To raise monoclonal antibodies, antibody-producing cells obtained from immunized animals (e.g., mice) are immortalized and screened, or screened first for the production of the desired antibody and then immortalized. For a discussion of general procedures of monoclonal antibody production see Harlow and Lane, Antibodies, A Laboratory Manual Cold Spring Harbor Publications, N.Y. (1988).

The antibodies raised by these techniques can be used in immunodiagnostic assays to detect or quantify the expression of gene products from the nucleic acids disclosed here. For instance, labeled monoclonal antibodies to polypeptides of the invention can be used to detect expression levels in a biological sample. For a review of the general procedures in diagnostic immunoassays, see Basic and Clinical Immunology 7th Edition D. Stites and A. Terr ed. (1991).

The polynucleotides of the invention are particularly useful for gene therapy techniques well known to those skilled in the art. Gene therapy as used herein refers to the multitude of techniques by which gene expression may be altered in cells. Such methods include, for instance, introduction of DNA encoding ribozymes or antisense nucleic acids to inhibit expression as well as introduction of functional wild-type genes to replace mutant genes (e.g., using wild-type GCAP genes to treat retinal degeneration). A number of suitable viral vectors are known. Such vectors include retroviral vectors (see Miller, Curr. Top. Microbiol. Immunol. 158: 1-24 (1992); Salmons and Gunzburg, Human Gene Therapy 4: 129-141 (1993); Miller et al., Methods in Enzymology 217: 581-599, (1994)) and adeno-associated vectors (reviewed in Carter, Curr. Opinion Biotech. 3: 533-539 (1992); Muzcyzka, Curr. Top. Microbiol. Immunol. 158: 97-129 (1992)). Other viral vectors that may be used within the methods include adenoviral vectors, herpes viral vectors and Sindbis viral vectors, as generally described in, e.g., Jolly, Cancer Gene Therapy 1:51-64 (1994); Latchman, Molec. Biotechnol. 2:179-195 (1994); and Johanning et al., Nucl. Acids Res. 23:1495-1501 (1995).

Delivery of nucleic acids linked to a heterologous promoter-enhancer element via liposomes is also known (see, e.g., Brigham, et al. (1989) Am. J. Med. Sci. 298:278-281; Nabel, et al. (1990) Science, 249:1285-1288; Hazinski, et al. (1991) Am. J. Resp. Cell Molec. Biol., 4:206-209; and Wang and Huang (1987) Proc. Natl. Acad. Sci. (USA), 84:7851-7855); coupled to ligand-specific, cation-based transport systems (Wu and Wu (1988) J. Biol. Chem., 263:14621-14624). Naked DNA expression vectors have also been described (Nabel et al. (1990), supra); Wolff et al. (1990) Science, 247:1465-1468).

The nucleic acids and encoded polypeptides of the invention can be used directedly to inhibit the endogenous genes or their gene products. For instance, Inhibitory nucleic acids may be used to specifically bind to a complementary nucleic acid sequence. By binding to the appropriate target sequence, an RNA-RNA, a DNA-DNA, or RNA-DNA duplex is formed. These nucleic acids are often termed “antisense” because they are usually complementary to the sense or coding strand of the gene, although approaches for use of “sense” nucleic acids have also been developed. The term “inhibitory nucleic acids” as used herein, refers to both “sense” and “antisense” nucleic acids. Inhibitory nucleic acid methods encompass a number of different approaches to altering expression of specific genes that operate by different mechanisms.

In brief, inhibitory nucleic acid therapy approaches can be classified into those that target DNA sequences, those that target RNA sequences (including pre-mRNA and mRNA), those that target proteins (sense strand approaches), and those that cause cleavage or chemical modification of the target nucleic acids (ribozymes). These different types of inhibitory nucleic acid technology are described, for instance, in Helene, C. and Toulme, J. (1990) Biochim. Biophys. Acta., 1049:99-125. Inhibitory nucleic acid complementary to regions of c-myc mRNA has been shown to inhibit c-myc protein expression in a human promyelocytic leukemia cell line, HL60, which overexpresses the c-myc protoncogene. See Wickstrom E. L., et al., (1988) PNAS (USA), 85:1028-1032 and Harel-Bellan, A., et al., (1988) Exp. Med., 168:2309-2318.

The encoded polypeptides of the invention can also be used to design molecules (peptidic or nonpeptidic) that inhibit the endogenous proteins by, for instance, inhibiting interaction between the protein and a second molecule specifically recognized by the protein. Methods for designing such molecules are well known to those skilled in the art.

For instance, polypeptides can be designed which have sequence identity with the encoded proteins or may comprise modifications (conservative or non-conservative) of the sequences. The modifications can be selected, for example, to alter their in vivo stability. For instance, inclusion of one or more D-amino acids in the peptide typically increases stability, particularly if the D-amino acid residues are substituted at one or both termini of the peptide sequence.

The polypeptides can also be modified by linkage to other molecules. For example, different N- or C-terminal groups may be introduced to alter the molecule's physical and/or chemical properties. Such alterations may be utilized to affect, for example, adhesion, stability, bio-availability, localization or detection of the molecules.

For diagnostic purposes, a wide variety of labels may be linked to the terminus, which may provide, directly or indirectly, a detectable signal. Thus, the polypeptides may be modified in a variety of ways for a variety of end purposes while still retaining biological activity.

EXAMPLES

The following examples are offered to illustrate, but not to limit the present invention.

Example 1 Prognostic Implications of Amplification of Chromosomal Region 20q13 in Breast Cancer

Patients and Tumor Material.

Tumor samples were obtained from 152 women who underwent surgery for breast cancer between 1987 and 1992 at the Tampere University or City Hospitals. One hundred and forty-two samples were from primary breast carcinomas and 11 from metastatic tumors. Specimens from both the primary tumor and a local metastasis were available from one patient. Ten of the primary tumors that were either in situ or mucinous carcinomas were excluded from the material, since the specimens were considered inadequate for FISH studies. Of the remaining 132 primary tumors, 128 were invasion ductal and 4 lobular carcinomas. The age of the patients ranged from 29 to 92 years (mean 61). Clinical follow-up was available from 129 patients. Median follow-up period was 45 months (range 1.4-1.77 months). Radiation therapy was given to 77 of the 129 patients (51 patients with positive and 26 with negative lymph nodes), and systemic adjuvant therapy to 36 patients (33 with endocrine and 3 with cytotoxic chemotherapy). Primary tumor size and axillary node involvement were determined according to the tumor-node metastasis (TNM) classification. The histopathological diagnosis was evaluated according to the World Health Organization (11). The carcinomas were graded on the basis of the tubular arrangement of cancer cells, nuclear atypia, and frequency of mitotic or hyperchromatic nuclear figures according to Bloom and Richardson, Br. J. Cancer, 11: 359-377 (1957).

Surgical biopsy specimens were frozen at −70° C. within 15 minutes of removal. Cryostat sections (5-6 μm) were prepared for intraoperative histopathological diagnosis, and additional thin sections were cut for immunohistochemical studies. One adjacent 200 μm thick section was cut for DNA flow cytometric and FISH studies.

Cell Preparation for FISH.

After histological verification that the biopsy specimens contained a high proportion of tumor cells, nuclei were isolated from 200 μm frozen sections according to a modified Vindelov procedure for DNA flow cytometry, fixed and dropped on slides for FISH analysis as described by Hyytinen et al., Cytometry 16: 93-99 (1994). Foreskin fibroblasts were used as negative controls in amplification studies and were prepared by harvesting cells at confluency to obtain G1 phase enriched interphase nuclei. All samples were fixed in methanol-acetic-acid (3:1).

Probes.

Five probes mapping to the 20q13 region were used (see Stokke, et al., Genomics, 26: 134-137 (1995)). The probes included P1-clones for melanocortin-3-receptor (probe MC3R, fractional length from p-arm telomere (Flpter 0.81) and phosphoenolpyruvate carboxy kinase (PCK, Flpter 0.84), as well as anonymous cosmid clones RMC20C026 (Flpter 0.79). In addition, RMC20C001 (Flpter 0.825) and RMC20C030 (Flpter 0.85) were used. Probe RMC20C001 was previously shown to define the region of maximum amplification (Tanner et al., Cancer Res, 54: 4257-4260 (1994)). One cosmid probe mapping to the proximal p-arm, RMC20C038 (FLpter 0.237) was used as a chromosome-specific reference probe. Test probes were labeled with biotin-14-dATP and the reference probe with digoxigenin-11-dUTP using nick translation (Kallioniemi et al., Proc. Natl Acad Sci USA, 89: 5321-5325 (1992)).

Fluorescence in situ Hybridization.

Two-color FISH was performed using biotin-labeled 20q13-specific probes and digoxigenin-labelled 20p reference probe essentially as described (Id.). Tumor samples were postfixed in 4% paraformaldtheyde/phosphate-buffered saline for 5 min at 4 C prior to hybridization, dehydrated in 70%, 85% and 100% ethanol, air dried, and incubated for 30 min at 80° C. Slides were denatured in a 70% formamide/2× standard saline citrate solution at 72-74° C. for 3 min, followed by a proteinase K digestion (0.5 μg/ml). The hybridization mixture contained 18 ng of each of the labeled probes and 10 μg human placental DNA. After hybridization, the probes were detected immunochemically with avidin-FITC and anti-digoxigenin Rhodamine. Slides were counterstained with 0.2 μM 4,6-diamidino-2-phenylindole (DAPI) in an antifade solution.

Fluorescence Microscopy and Scoring of Signals in Interphase Nuclei.

A Nikon fluorescence microscope equipped with double band-bass filters (Chromatechnology, Brattleboro, Ver., USA) and 63× objective (NA 1.3) was used for simultaneous visualization of FITC and Rhodamine signals. At least 50 non-overlapping nuclei with intact morphology based on the DAPI counterstaining were scored to determine the number of test and reference probe hybridization signals. Leukocytes infiltrating the tumor were excluded from analysis. Control hybridizations to normal fibroblast interphase nuclei were done to ascertain that the probes recognized a single copy target and that the hybridization efficiencies of the test and reference probes were similar.

The scoring results were expressed both as the mean number of hybridization signals per cell and as mean level of amplification (=mean of number of signals relative to the number of reference probe signals).

DNA Flow Cytometry and Steroid Receptor Analyses.

DNA flow cytometry was performed from frozen 200 μm sections as described by Kallioniemi, Cytometry 9: 164-169 (1988). Analysis was carried out using an EPICS C flow cytometer (Coulter Electronics Inc., Hialeah, Fla., USA) and the MultiCycle program (Phoenix Flow Systems, San Diego, Calif., USA). DNA-index over 1.07 (in over 20% of cells) was used as a criterion for DNA aneuploidy. In DNA aneuploid histograms, the S-phase was analyzed only from the aneuploid clone. Cell cycle evaluation was successful in 86% (108/126) of the tumors.

Estrogen (ER) and progesterone (PR) receptors were detected immunohistochemically from cryostat sections as previously described (17). The staining results were semiquantitatively evaluated and a histoscore greater than or equal to 100 was considered positive for both ER and PR (17).

Statistical Methods

Contingency tables were analyzed with Chi square test for trend.

Association between S-phase fraction (continuous variable) and 20q13 amplification was analyzed with Kruskal-Wallis test. Analysis of disease-free survival was performed using the BMDPIL program and Mautel-Cox test and Cox's proportional hazards model (BMDP2L program) was used in multivariate regression analysis (Dixon BMDP Statistical Software, London, Berkeley, Los Angeles; University of California Press, (1981)).

Amplification of 20q13 in Primary Breast Carcinomas by Fluorescence in situ Hybridization.

The minimal region probe RMC20C001 was used in FISH analysis to assess the 20q13 amplification. FISH was used to analyze both the total number of signals in individual tumor cells and to determine the mean level of amplification (mean copy number with the RMC20C001 probe relative to a 20p-reference probe). In addition, the distribution of the number of signals in the tumor nuclei was also assessed. Tumors were classified into three categories: no. low and high level of amplification. Tumors classified as not amplified showed less than 1.5 than 1.5 fold-copy number of the RMC20C001 as compared to the p-arm control. Those classified as having low-level amplification had 1.5-3-fold average level of amplification. Tumors showing over 3-fold average level of amplification were classified as highly amplified.

The highly amplified tumors often showed extensive intratumor heterogeneity with up to 40 signals in individual tumor cells. In highly amplified tumors, the RM C20C001 probe signals were always arranged in clusters by FISH, which indicates location of the amplified DNA sequences in close proximity to one another e.g. in a tandem array. Low level 20q13 amplification was found in 29 of the 132 primary tumors (22%), whereas nine cases (6.8%) showed high level amplification. The overall prevalence of increased copy number in 20q13 was thus 29% (38/132).

Defining the Minimal Region of Amplification.

The average copy number of four probes flanking RMC20C001 was determined in the nine highly amplified tumors. The flanking probes tested were malanocortin-3-receptor (MC3R, FLpter 0.81), phosphoenolpyruvate carboxykinase (PCK, 0.84), RMC20C026 (0.79) and RMC20C030 (0.85). The amplicon size and location varied slightly from one tumor to another but RMC20C001 was the only probe consistently highly amplified in all nine cases.

Association of 20q13 Amplification with Pathological and Biological Features.

The 20q13 amplification was significantly associated with high histologic grade of the tumors (p=0.01). This correlation was seen both in moderately and highly amplified tumors (Table 4). Amplification of 20q13 was also significantly associated with aneuploidy as determined by DNA flow cytometry (p=0.01, Table 4) The mean cell proliferation activity, measured as the percentage of cells in the S-phase fraction, increased (p=0.0085 by Kruskal-Wallis test) with the level of amplification in tumors with no, low and high levels of amplification (Table 4). No association was found with the age of the patient, primary tumor size, axillary nodal or steroid hormone-receptor status (Table 4).

TABLE 4 Clinicopathological correlations of amplification at chromosomal region 20q13 in 132 primary breast cancers. 20q13 Amplification status HIGH NO LOW LEVEL LEVEL Pathobiologic Number of Number of Number of feature patients (%) patients (%) patients (%) p-value¹ All primary 94 (71%) 29 (22%) 9 (6.8%) tumors Age of patients <50 years 17 (65%)  6 (23%) 3 (12%) ≧50 years 77 (73%) 23 (22%) 6 (5.7%) .39 Tumor size <2 cm 33 (79%)  7 (17%) 2 (4.8%) ≧2 cm 58 (67%) 22 (25%) 7 (8.0%) .16 Nodal status Negative 49 (67%) 19 (26%) 5 (6.8%) Positive 41 (75%) 10 (18%) 4 (7.3%) .41 Histologic grade I-II 72 (76%) 18 (19%) 5 (5.3%) III 16 (52%) 11 (35%) 4 (13%) .01 Estrogen receptor status Negative 30 (67%) 10 (22%) 5 (11%) Positive 59 (72%) 19 (23%) 4 (4.9%) .42 Progesterone receptor status Negative 57 (69%) 20 (24%) 6 (7.2%) Positive 32 (74%)  8 (19%) 3 (7.0%) .53 DNA ploidy Diploid 45 (82%)  8 (14.5%) 2 (3.6%) .01 Aneuploid 44 (62%) 20 (28%) 7 (10%) S-phase function mean ± SD mean ± SD mean ± SD .0085¹ (%) 9.9 ⊥ 7.2 12.6 ± 6.7 19.0 ± 10.5 ¹Kruskal-Wallis Test.

Relationship Between 20q13 Amplification and Disease-free Survival.

Disease-free survival of patients with high-level 20q13 amplification was significantly shorter than for patients with no or only low-level amplification (p-0.04). Disease-free survival of patients with moderately amplified tumors did not differ significantly from that of patients with no amplification. Among the node-negative patients (n=79), high level 20q13 amplification was a highly significant prognostic factor for shorter disease-free survival (p=0.002), even in multivariate Cox's regression analysis (p=0.026) after adjustment for tumor size ER, PR grade, ploidy and S-phase fraction.

20q13 Amplification in Metastatic Breast Tumors.

Two of 11 metastatic breast tumors had low level and one high level 20q13 amplification. Thus, the overall prevalence (27%) of increased 20q13 copy number in metastatic tumors was a similar to that observed in the primary tumors. Both a primary and a metastatic tumor specimens were available from one of the patients. This 29-year old patient developed a pectoral muscle infiltrating metastasis eight months after total mastectomy. The patient did not receive adjuvant or radiation therapy after mastectomy. The majority of tumor cells in the primary tumor showed a low level amplification, although individual tumor cells (less than 5% of total) contained 8-20 copies per cell by FISH. In contrast, all tumor cells from metastasis showed high level 20q13 amplification (12-50 copies per cell). The absolute copy number of the reference probe remained the same suggesting that high level amplification was not a result of an increased degree of aneuploidy.

Diagnostic and Prognostic Value of the 20q13 Amplification.

The present findings suggest that the newly-discovered 20q13 amplification may be an important component of the genetic progression pathway of certain breast carcinomas. Specifically, the foregoing experiments establish that: 1) High-level 20q13 amplification, detected in 7% of the tumors, was significantly associated with decreased disease-free survival in node-negative breast cancer patients, as well as with indirect indicators of high-malignant potential, such as high grade and S-phase fraction. 2) Low-level amplification, which was much more common, was also associated with clinicopathological features of aggressive tumors, but was not prognostically significant. 3) The level of amplification of RMC20C001 remains higher than amplification of nearby candidate genes and loci indicating that a novel oncogene is located in the vicinity of RMC20C001.

High-level 20q13 amplification was defined by the presence of more than 3-fold higher copy number of the 20q13 amplification is somewhat lower than the amplification frequencies reported for some of the other breast cancer oncogenes, such as ERBB2 (17q12) and Cyclin-D (11q13) (Borg et al., Oncogene, 6: 137-143 (1991), Van de Vijver et al. Adv. Canc. Res., 61: 25-56 (1993)). However, similar to what has been previously found with these other oncogenes (Swab, et al., Genes Chrom. Canc., 1: 181-193 (1990), Borg et al., supra.), high-level 20q13 amplification was more common in tumors with high grade or high S-phase fraction and in cases with poor prognosis. Although only a small number of node-negative patients was analyzed, our results suggest that 20q13 amplification might have independent role as a prognostic indicator. Studies to address this question in large patient materials are warranted. Moreover, based on these survival correlations, the currently unknown, putative oncogene amplified in this locus may confer an aggressive phenotype. Thus, cloning of this gene is an important goal. Based on the association of amplification with highly proliferative tumors one could hypothesize a role for this gene in the growth regulation of the cell.

The role of the low-level 20q13 amplification as a significant event in tumor progression appears less clear. Low-level amplification was defined as 1.5-3-fold increased average copy number of the 20q13 probe relative to the p-arm control. In addition, these tumors characteristically lacked individual tumor cells with very high copy numbers, and showed a scattered, not clustered, appearance of the signals. Accurate distinction between high and low level 20q13 amplification can only be reliably done by FISH, whereas Southern and slot blot analyses are likely to be able to detect only high-level amplification, in which substantial elevation of the average gene copy number takes place. This distinction is important, because only the high amplified tumors were associated with adverse clinical outcome. Tumors with low-level 20q13 amplification appeared to have many clinicopathological features that were in between of those found for tumors with no and those with high level amplification. For example, the average tumor S-phase fraction was lowest in the non-amplified tumors and highest in the highly amplified tumors. One possibility is that low-level amplification precedes the development of high level amplification. This has been shown to be the case, e.g., in the development of drug resistance-gene amplification in vitro (Stark, Adv. Canc. Res., 61: 87-113 (1993)). Evidence supporting this hypothesis was found in one of our patients, whose local metastasis contained a much higher level of 20q13 amplification than the primary tumor operated 8 months earlier.

Finally, our previous paper reported a 1.5 Mb critical region defined by RMC20C001 probe and exclusion of candidate genes in breast cancer cell lines and in a limited number of primary breast tumors. Results of the present study confirm these findings by showing conclusively in a larger set of primary tumors that the critical region of amplification is indeed defined by this probe.

The present data thus suggest that the high-level 20q13 amplification may be a significant step in the progression of certain breast tumors to a more malignant phenotype. The clinical and prognostic implications of 20q13 amplification are striking and location of the minimal region of amplification at 20q13 has now been defined.

It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated by reference for all purposes.

Discussion of the Accompanying Sequence Listing

SEQ ID NOs: 1-10 and 12-13 provide nucleic acid sequences. In each case, the information is presented as a DNA sequence. One of skill will readily understand that the sequence also describes the corresponding RNA (i.e., by substitution of the T residues with U residues) and a variety of conservatively modified variations thereof. The complementary sequence is fully described by comparison to the existing sequence, i.e., the complementary sequence is obtained by using standard base pairing rules for DNA (e.g., A to T, C to G). In addition, the nucleic acid sequence provides the corresponding amino acid sequence by translating the given DNA sequence using the genetic code.

For SEQ ID NO 11, the information is presented as a polypeptide sequence. One of skill will readily understand that the sequence also describes all of the corresponding RNA and DNA sequences which encode the polypeptide, by conversion of the amino acid sequence into the corresponding nucleotide sequence using the genetic code, by alternately assigning each possible codon in each possible codon position. Similarly, each nucleic acid sequence which is provided also inherently provides all of the nucleic acids which encode the same protein, since one of skill simply translates a selected nucleic acid into a protein and then uses the genetic code to reverse translate all possible nucleic acids from the amino acid sequence.

The sequences also provide a variety of conservatively modified variations by substituting appropriate residues with the exemplar conservative amino acid substitutions provided, e.g., in the Definitions section above.

59 1 3000 DNA Artificial Sequence Description of Artificial Sequence3bf4 1 ccgccggccg gggcgcctgg ctgcactcag cgccggagcc gggagctagc ggccgccgcc 60 atgtcccacc agaccggcat ccaagcaagt gaagatgtta aagagatctt tgccagagcc 120 agaaatggaa agtacagact tctgaaaata tctattgaaa atgagcaact tgtgattgga 180 tcatatagtc agccttcaga ttcctgggat aaggattatg attcctttgt tttacccctg 240 ttggaggaca aacaaccatg ctatatatta ttcaggttag attctcagaa tgcccaggga 300 tatgaatgga tattcattgc atggtctcca gatcattctc atgttcgtca aaaaatgttg 360 tatgcagcaa caagagcaac tctgaagaag gaatttggag gtggccacat taaagatgaa 420 gtatttggaa cagtaaagga agatgtatca ttacatggat ataaaaaata cttgctgtca 480 caatcttccc ctgccccact gactgcagct gaggaagaac tacgacagat taaaatcaat 540 gaggtacaga ctgacgtggg tgtggacact aagcatcaaa cactacaagg agtagcattt 600 cccatttctc gagaagcctt tcaggctttg gaaaaattga ataatagaca gctcaactat 660 gtgcagttgg aaatagatat aaaaaatgaa attataattt tggccaacac aacaaataca 720 gaactgaaag atttgccaaa gaggattccc aaggattcag ctcgttacca tttctttctg 780 tataaacatt cccatgaagg agactattta gagtccatag tttttattta ttcaatgcct 840 ggatacacat gcagtataag agagcggatg ctgtattcta gctgcaagag ccgtctgcta 900 gaaattgtag aaagacaact acaaatggat gtaattagaa agatcgagat agacaatggg 960 gatgagttga ctgcagactt cctttatgaa gaagtacatc ccaagcagca tgcacacaag 1020 caaagttttg caaaaccaaa aggtcctgca ggaaaaagag gaattcgaag actaattagg 1080 ggcccagcgg aaactgaagc tactactgat taaagtcatc acattaaaca ttgtaatact 1140 agttttttaa aagtccagct tttagtacag gagaactgaa atcattccat gttgatataa 1200 agtagggaaa aaaattgtac tttttggaaa atagcacttt tcacttctgt gtgtttttaa 1260 aattaatgtt atagaagact catgatttct atttttgagt taaagctaga aaagggttca 1320 acataatgtt taattttgtc acactgtttt catagcgttg attccacact tcaaatactt 1380 cttaaaattt tatacagttg ggccagttct agaaagtctg atgtctcaaa gggtaaactt 1440 actactttct tgtgggacag aaagacctta aaatattcat attacttaat gaatatgtta 1500 aggaccaggc tagagtattt tctaagctgg aaacttagtg tgccttggaa aagccgcaag 1560 ttgcttactc cgagtagctg tgctagctct gtcagactgt aggatcatgt ctgcaacttt 1620 tagaaatagt gctttatatt gcagcagtct tttatatttg actttttttt aatagcatta 1680 aaattgcaga tcagctcact ctgaaacttt aagggtacca gatattttct atactgcagg 1740 atttctgatg acattgaaag actttaaaca gccttagtaa attatctttc taatgctctg 1800 tgaggccaaa catttatgtt cagattgaaa tttaaattaa tatcattcaa aaggaaacaa 1860 aaaatgttga gttttaaaaa tcaggattga cttttttctc caaaaccata catttatggg 1920 caaattgtgt tctttatcac ttccgagcaa atactcagat ttaaaattac tttaaagtcc 1980 tggtacttaa caggctaacg tagataaaca ccttaataat ctcagttaat actgtatttc 2040 aaaacacatt taactgtttt ctaatgcttt gcattatcag ttacaaccta gagagatttt 2100 gagcctcata tttctttgat acttgaaata gagggagcta gaacacttaa tgtttaatct 2160 gttaaacctg ctgcaagagc cataactttg aggcattttc taaatgaact gtggggatcc 2220 aggatttgta atttcttgat ctaaacttta tgctgcataa atcacttatc ggaaatgcac 2280 atttcatagt gtgaagcact catttctaaa ccttattatc taaggtaata tatgcacctt 2340 tcagaaattt gtgttcgagt aagtaaagca tattagaata attgtgggtt gacagatttt 2400 taaaatagaa tttagagtat ttggggtttt gtttgtttac aaataatcag actataatat 2460 ttaaacatgc aaaataactg acaataatgt tgcacttgtt tactaaagat ataagttgtt 2520 ccatgggtgt acacgtagac agacacacat acacccaaat tattgcatta agaatcctgg 2580 agcagaccat agctgaagct gttattttca gtcaggaaga ctacctgtca tgaaggtata 2640 aaataattta gaagtgaatg tttttctgta ccatctatgt gcaattatac tctaaattcc 2700 actacactac attaaagtaa atggacattc cagaatatag atgtgattat agtcttaaac 2760 taattattat taaaccaatg attgctgaaa atcagtgatg catttgttat agagtataac 2820 tcatcgttta cagtatgttt tagttggcag tatcatacct agatggtgaa taacatattc 2880 ccagtaaatt tatatagcag tgaagaatta catgccttct ggtggacatt ttataagtgc 2940 attttatatc acaataaaaa ttttttctct ttaaaaaaaa aaaacaagaa aaaaaaaaaa 3000 2 723 DNA Artificial Sequence Description of Artificial Sequence1b11 2 tggaagctgt catggttacc gtctctaacg ttggactctt aagaaaatga ttattcctgg 60 tttctagaca ggccaaatgt aattcaccta cgtggcagat taaagaggtg ggcttactag 120 atttgattgg gtattgagca tgctctgaat gacagtcccc aaaaaggacc tcttatccgt 180 tcttcccctt ggggaagggc ttttgccact tccatgtcaa tgtggcagtt gagcttggaa 240 attggtgcgt tgtacaacat aagcattact tctccaagat gtgcctgtgt agaaatggtc 300 atagattcaa aactgtagct actatgtgga caggggggca gcaaggaccc cactttgtaa 360 aacatgtttt gggggaatgt tttgtttttc attttcttat tacctggcaa aataatccag 420 gtggtgtgtg agtcaccagt agagattata aagtccaagg aagtagaatc agccttacaa 480 acagtggacc tcaacgaagg agatgctgca cctgaaccca cwgaagcgaa actcaaaaga 540 gaagaaagca aaccaagaac ctctctgatg rcgtttctca gacaaatggt aagcccctta 600 cttccagtat aggaaaccta agatacctag agcggctttt gggaacaatg ggctcatgcc 660 acaggtagta ggagacataa ttgtagctgg tgtgtatgga atgtgaatgg aatatggatt 720 gcg 723 3 1507 DNA Artificial Sequence Description of Artificial Sequencecc49 3 gcaggttgct gggattgact tcttgctcaa ttgaaacact cattcaatgg agacaaagag 60 cactaatgct ttgtgctgat tcatatttga atcgaggcat tgggaaccct gtatgccttg 120 tttgtggaaa gaaccagtga caccatcact gagcttccta aaagttcgaa gaagttagag 180 gactatacac tttcttttga acttttataa taaatatttg ctctggtttt ggaacccagg 240 actgttagag ggtgagtgac aggtcttaca gtggccttaa tccaactcca gaaattgccc 300 aacggaactt tgagattata tgcaatcgaa agtgacagga aacatgccaa ctcaatccct 360 cttaatgtac atggatggcc aagagtgatt ggcagctctc ttgccagtcc gatggagatg 420 gagatgcctt gtcaatgaaa gggcccnctg ttgtcaattc cgagctacac aaagaaaaaa 480 atgtcaatcc gaatcgaggg gaatatgccc ttggattgca tgttctgcag ccagaccttc 540 acacattcag aagaccttaa taaacatgtc ttaatgcaac accggcctac cctctgtgaa 600 ccagcagttc ttcgggttga agcagagtat ctcagtccgc ttgataaaag tcaagtgcga 660 acagaacctc ccaaggaaaa gaattgcaag gaaaatgaat ttagctgtga ggtatgtggg 720 cagacattta gagtcgcttt tgatgttgag atccacatga gaacacacaa agattctttc 780 acttacgggt gtaacatgtg cggaagaaga ttcaaggagc cttggtttct taaaaatcac 840 atgcggacrc ataatggcaa atcgggggcc agaagcaaac tgcagcaagg cttggagagt 900 agtccagcaa cgatcaacga ggtcgtccag gtgcacgcgg ccgagagcat ctcctctcct 960 tgcaaaatct gcatggtttg tggcttccta tttccaaata aagaaagtct aattgagcac 1020 cgcaaggtgc acaccaaaaa aactgctttc ggtaccagca gcgcgcagac agactctcca 1080 caaggaggaa tgccgtcctc gagggaggac ttcctgcagt tgttcaactt gagaccaaaa 1140 tctcaccctg aaacggggaa gaagcctgtc agatgcatcc ctcagctcga tccgttcacc 1200 accttccagg cttggcakct ggctaccaaa ggaawagttg ccatttgcca agaagtgaag 1260 gaattggggc aagaagggag caccgacaac gacgattcga gttccgagaa ggagcttgga 1320 gaaacaaata agaaccattg tgcaggcctc tcgcaagaga aagagaagtg caaacactcc 1380 cacggcgaag cgccctccgt ggacgcggat cccaagttac ccagtagcaa ggagaagccc 1440 actcactgct ccgagtgcgg caaagctttc agaacctacc accagctggt cttgcactcc 1500 agggtcc 1507 4 2605 DNA Artificial Sequence Description of Artificial Sequencecc43 4 caagctcgaa attaaccctc actaaaggga acaaaagctg gagctccacc gcggtggcgg 60 ccgctctaga actagtggat cccccgggct gcaggaattc ggcacgagct gggctactac 120 gatggcgatg agtttcgagt ggccgtggca gtatcgcttc ccacccttct ttacgttaca 180 accgaatgtg gacactcggc agaagcagct ggccgcctgg tgctcgctgg tcctgtcctt 240 ctgccgcctg cacaaacagt ccagcatgac ggtgatggaa gctcaggaga gcccgctctt 300 caacaacgtc aagctacagc gaaagcttcc tgtggagtcg atccagattg tattagagga 360 actgaggaag aaagggaacc tcgagtggtt ggataagagc aagtccagct tcctgatcat 420 gtggcggagg ccagaagaat gggggaaact catctatcag tgggtttcca ggagtggcca 480 gaacaactcc gtctttaccc tgtatgaact gactaatggg gaagacacag aggatgagga 540 gttccacggg ctggatgaag ccactctact gcgggctctg caggccctac agcaggagca 600 caaggccgag atcatcactg tcagcgatgg ccgaggcgtc aagttcttct agcagggacc 660 tgtctccctt tacttcttac ctcccacctt tccagggctt tcaaaaggag acagacccag 720 tgtcccccaa agactggatc tgtgactcca ccagactcaa aaggactcca gtcctgaagg 780 ctgggacctg gggatgggtt tctcacaccc catatgtctg tcccttggat agggtgaggc 840 tgaagcacca gggagaaaat atgtgcttct tctcgcccta cctcctttcc catcctagac 900 tgtccttgag ccagggtctg taaacctgac actttatatg tgttcacaca tgtaagtaca 960 tacacacatg cgcctgcagc acatgcttct gtctcctcct cctcccaccc ctttagctgc 1020 tgttgcctcc cttctcaggc tggtgctgga tccttcctag gggatggggg aagccctggc 1080 tgcaggcagc cttccaggca atatgaagat aggaggccca cgggcctggc agtgagaggt 1140 gtggccccac accgatttat gatattaaaa tctcaactcc caaaaaaaaa aaaaaaaaaa 1200 ctgagactag ttctctctct ctcgagaact agtctcgagt tttttttttt tttttttttt 1260 tttttttttt tttttttttg gctttaagga tttatttatt gtttcctctt tacagtgtcc 1320 acttttctct acttaatact actttccagt ctcagaagcc cagagggaaa aaaaaaagac 1380 catgaatctt cctctcccag attaaagtac acactttgga aaacagattg gaaaaccttt 1440 ctgaaaaaag ttgactgaaa ctccaaacca acatgccata ttgttgatgt tgctcatgaa 1500 aattgttaaa aacctgttct agataaagaa cagtctcaag tttttgtaca gcctacacat 1560 agtacaaggg tcccctatga tgattcttct gtaggacgaa ataatgtaat tttttcagtt 1620 tctggtttat aactctctcg atctcagagt tgactgatta aaacacctac tcatgcaaca 1680 gagaataaag cactcatatt tttataaatt atatggacca aactattttg gaaatcttat 1740 ctattggaga cacaatatgc tggactaaag caataattat tttattctca atgtctgtgc 1800 taacctcaat gacttagaat gctttgctat attttgcctc tatgcctcaa ccacactggc 1860 tttcttttag ctcttgaaca agccaaactg cttcctgcct caggaccaga tattttggga 1920 cttctcttaa gaattctatt tccttaattc tttatctggg taacttagtt ttatccaaca 1980 cttcagatcc tgccgtaaaa actcttctta tagaagcctg tcatgacact gtctctcttc 2040 tccaacatac tcaccagcac acatgtagac tagattagaa cctcctgttt ttctttttca 2100 tacttttctc tatcatgctt ccctccatta taatattttt attatgtgtg tgaatgtctg 2160 ccccaagtca gtttcctcac taaactataa actccgtaaa gctgggatcc ttccaatttt 2220 gatcaccact tagtacagta ggaacacagt aaagattcaa ttggtatttg tggaatgaat 2280 gaatgaattg ttttgctagt aaagtctggg ggaacccagg tgagaagagc ctagaaagca 2340 ggtcgaatcc aaggctagat agacttagtg ttactcaaga aagggtagcc tgaaaataaa 2400 ggttcaaatt atagtcaaga atagtcaaga catgggcaag acaagagtgc tgctcgtgcc 2460 gaattcgata tcaagcttat cgataccgtc gacctcgagg gggggcccgg tacccaattc 2520 gccctatagt gagtcgtatt acaattcact ggccgtcgtt ttacaacgtc gtgactggga 2580 aaaccctggc gttacccaac ttaat 2605 5 1288 DNA Artificial Sequence Description of Artificial Sequence41.1 5 gagggcagcg agaaggagaa accccagccc ctggagccca catctgctct gagcaatggg 60 tgcgccctcg ccaaccacgc cccggccctg ccatgcatca acccactcag cgccctgcag 120 tccgtcctga acaatcactt gggcaaagcc acggagccct tgcgctcacc ttcctgctcc 180 agcccaagtt caagcacaat ttccatgttc cacaagtcga atctcaatgt catggacaag 240 ccggtcttga gtcctgcctc cacaaggtca gccagcgtgt ccaggcgcta cctgtttgag 300 aacagcgatc agcccattga cctgaccaag tccaaaagca agaaagccga gtcctcgcaa 360 gcacaatctt gtatgtcccc acctcagaag cacgctctgt ctgacatcgc cgacatggtc 420 aaagtcctcc ccaaagccac caccccaaag ccagcctcct cctccagggt cccccccatg 480 aagctggaaa tggatgtcag gcgctttgag gatgtctcca gtgaagtctc aactttgcat 540 aaaagaaaag gccggcagtc caactggaat cctcagcatc ttctgattct acaagcccag 600 tttgcctcga gcctcttcca gacatcagag ggcaaatacc tgctgtctga tctgggccca 660 caagagcgta tgcaaatctc taagtttacg ggactctcaa tgaccactat cagtcactgg 720 ctggccaacg tcaagtacca gcttaggaaa acgggcggga caaaatttct gaaaaacatg 780 gacaaaggcc accccatctt ttattgcagt gactgtgcct cccagttcag aaccccttct 840 acctacatca gtcacttaga atctcacctg ggtttccaaa tgaaggacat gacccgcttg 900 tcagtggacc agcaaagcaa ggtggagcaa gagatctccc gggtatcgtc ggctcagagg 960 tctccagaaa caatagctgc cgaagaggac acagactcta aattcaagtg taagttgtgc 1020 tgtcggacat ttgtgagcaa acatgcggta aaactccacc taagcaaaac gcacagcaag 1080 tcacccgaac accattcaca gtttgtaaca gacgtggatg aagaatagct ctgcaggacg 1140 aatgccttag tttccacttt ccagcctgga tcccctcaca ctgaaccctt cttcgttgca 1200 ccatcctgct tctgacattg aactcattga actcctcctg acaccctggc tctgagaaga 1260 ctgccaaaaa aaaaaaaaaa aaaaattc 1288 6 2821 DNA Artificial Sequence Description of Artificial SequenceGCAP 6 atcctaagac gcacagcctg ggaagccagc actggggaag tggtgctgag ggatgtgggt 60 cactggggtg aaggtggagc tttcagggtc tcccgtcaat gcagctgagt tttctttggc 120 agggaattta ccagctgaag aaagcctgcc ggcgagagct acaaactgag caaggccagc 180 tgctcacacc cgaggaggtc gtggacagga tcttcctcct ggtggatgag aatggagatg 240 gtaagagggg cagagatggg gagagtgctg tccactctgc atcatcgcca ctttctggcc 300 gcacgtcctt gggcaaggcc ctccaccttc caaccctggg gtcctcatct gtgagaaggc 360 tgtggagaag atgtcatgaa ctaacaaagg gactcatgag cacgtgtttg taggagtgac 420 taaaagtcct acaggagttg ctgatggagg ccaggcacgc agaatagaaa gaataggaac 480 tttggagtca ggcagggagt gatatattga gcttctcgtc ctagtctcaa tttcctcatc 540 tggaaaatgg ggataataat agtggttgag aggaatgaat aggataatgt gtttaagagc 600 aggcataggg tagacctcca ttcaggctgc ttgggctttc ctccctgtag cccaaagccc 660 agcctcaggg ctatgtgggg agagagctgg cttggaatac acacttgagc cctccagctc 720 tctcagctcc acccagcatt tccgtggtac catgcgcaaa agtaaaactt caattcatca 780 gcaaagaaag ccccttaaag gtggcaggag actcctggag attcagacac ctgacaagcc 840 gcaagcttga ggtctgagac tgcaggatag ttggcataag acgtgtaggc gcatcctggg 900 agcgaggtct ctcctcctgc ccccagaccc aggtctcccc ttcttctaca tgaccacctc 960 tcctccccct tgctcaggcc agctgtctct gaacgagttt gttgaaggtg cccgtcggga 1020 caagtgggtg atgaagatgc tgcagatgga catgaatccc agcagctggc tcgctcagca 1080 gagacggaaa agtgccatgt tctgaggagt ctggggcccc tccacgactc caggctcacc 1140 caggtttcca gggtagtagg agggtcccct ggctcagcct gctcatgccc actcttcccc 1200 tggtgttgac ttcctggcac cccctgtgca gggctgagtg gggatgggga agggctgctg 1260 ggtttgaagt ggccaacagg gcatagtcca ttttggagga gtccctggga tggtgaaggg 1320 aattcagtta cttttcctgt tcagccgctc ctgggaggac tgtgccttgg ctgggtggtt 1380 gtggggctcc cacagtttct gggtgttctc agttggaagc aagagccaac tgaggggtga 1440 gggtcccaca gaccaaatca gaaatgagaa cacaaagact ggtaggaggc aggggtggga 1500 gggtgttgag actgaagaaa aggcaggagt tgccgggcac ggtggctcac gcctgtaatc 1560 ccagcacttt gggaggccga ggcgggcaga tcacgaggtc aggagatcga gaccatcctg 1620 gctaacacgg ggtgaaaccc cgtctctact aaaaatacaa aaaatcagcc gggtgaggtg 1680 gcgggcgcct gtagtcccag ctactcagga ggctgaggca agagaatggc gtgaacccca 1740 gggggccgag cctacagtga gccgagattg cgccactgca ctccagcctg gacgacagtg 1800 agactccgtc tcaaaaaaaa aaaaagaaag aaaagaaaag gcaggagttt tggggggcag 1860 ggggcagcaa taattctata acttccggga tgctgagggg cgttcatggg gaggaccctg 1920 gcctcctcct ccccaaggca tcctcaccag tggtgtcaac aggaaaaatg gcagcaaata 1980 cgctgcaggc tgtggtcttt ctgcctttga aagggtcagc tgtacttaaa gggactgttt 2040 cagctctgcc tgggtgctgc tctgggaccc cctgctgcca acccaccact cccccaacaa 2100 tcctctcttt ccatccatat cccccagtat ggaccttcca caactcccag ccataagctg 2160 aatgtttctc tttaaaggat ggagaaaact tctgtctgtc tctggcaaga attgggggac 2220 tgttgactgg gattgtgggc tgggcttggc ttctaactgc tgtgtgaccc aagacagcca 2280 cttctcctcc ctaaccttgg ttatgtcttg gcagcacagt gagcaggtcg gactaggcga 2340 acagttttgg attattgtgt ttttagatgt ggaattattt tttgttatat aaactcttat 2400 gtgtaacccc aatatagaaa ctagattaaa agggagtctc tctggttgaa aggggagctg 2460 agtaccctct ggaactggag gcacctctga aaaaagcaaa ctgaaaacca gtgccctggg 2520 tcactgttac tcctataaga cagtttaaag tgagacctgg aaaaacattt gctttacctt 2580 gaatagatag gtttttatgt tggtatataa gaaataaaac taacctatta accctgagac 2640 tttacaggtg tgttatttca tatgatagtc atataaaatt tcctttagac atcaatttta 2700 ggtaaaaaat aattgattag aaaaatattg gccaggtgca gcagctcaca cctgcaatcc 2760 caggactttg ggaggccgag gcgggtggat cacctgaggt caggggttca agaccagcct 2820 g 2821 7 1205 DNA Artificial Sequence Description of Artificial Sequence1b4 7 gcgcgcgtga gtccgccccc ccagtcacgt gaccgctgac tcggggcgtt ctccactatc 60 gcttacctac ctccctctgc aggaacccgg cgatatggct gccgctgtgc cccgcgccgc 120 atttctctcc ccgctgcttc ccttctcctg ggcttcctgc tcctctccgc tccgcatggc 180 ggcagcggcc tgcacaccaa ggcgcccttc ccctggatac ggtcactttc tacaaggtca 240 ttcccaaaag caagttcgtc tggtgaagtt cgacacccag tacccctacg gtgagaagca 300 ggatgagttc aagcgtcttc tgaaaactcg gcttccagcg atgatctctt ggtggcagag 360 gtggggatct cagattatgt gacaagctga acatggagct gagtgagaaa tacaagctgg 420 acaaagagag ctacccatct tctacctctt ccgggatggg gactttgaga acccagtccc 480 atacactggg gcagttaggt tggagccatc cagcgctggc tgaaggggca aggggtctac 540 ctaggtatgc ctggtgcctg cctgtatacg acgccctggc cggggagttc atcagggcct 600 ctggtgtgga ggccgccagg ccctcttgaa gcaggggcaa gataacctct caagtgtgaa 660 ggagactcag aagagtgggc cgagcaatac ctgaagatca tggggaagat cttagaccaa 720 ggggagcact tccagcatca gagatgacac ggatcgccag gctgattgag aagaacaaga 780 tgagtgacgg cagaaggagg agctccagaa gagcttaaac atcctgactg ccttccagaa 840 gaagggggcc gagaaagagg agctgtaaaa aggctgtctg tgattttcca gggtttggtg 900 ggggtaggga gggganagtt aacctgctgg ctgtgantcc cttgtggaat ataagggggy 960 mskgggaaaa gwggtactaa cccacgattc tgagccctga gtatgcctgg acattgatgc 1020 taacatgacc atgcttggga tgtctctagc tggtctgggg atagctggag cacttactca 1080 ggtggctggt gaaatgacac ctcagaagga atgagtgcta tagagaggag agaggagtgt 1140 actgcccagg tctttgacag atgtaattct cattcaatta aagtttcagt gttttggtta 1200 agtgg 1205 8 455 DNA Artificial Sequence Description of Artificial Sequence20sa7 8 gaaatcagaa gtttaatatg acacaattaa atatatttgt atatctcaca ccggagnttc 60 tcttcaaaca taaggagtta gaaattacaa gtaggcatat gcttcctata ttcagataaa 120 ttcatttcga ttaattaaat tccagataga gagaagtaat tttcggaaaa gaaatgatag 180 ctatattaaa gcagatattc attacaatac catgtagaga cataagcaat attttggcat 240 cattctgtcc gctcagtagg ccgtgttccc tctggtaggg cctttggaga gtaccatcta 300 tctaagatgg aggaatgctg tgggaagggc gggatggagg tgcgttttct acgctgaacc 360 ccacacagga aatctgcagc ccacacagct gcctctgcgc cgccttccat gtgatcatcc 420 tggtcaatga agtgaattgt cctatttcng ggggt 455 9 10365 DNA Artificial Sequence Description of Artificial SequenceGenomic Sequence encoding ZABC1 9 ccatcatatt tcttattttt ttgggcggag aggggagact tgctctgttg cccaggctgg 60 accagtggtg cgatcttggc tcactgcaac ctccacctcc tgggttcaag tgattcccaa 120 atagctggga ttacaggtgt gtattaccat gcccagctaa tttttgtatt tttagcagat 180 aaggggtttc accatgttgg ccaggctggt ctccaactcc tggcctcatg tgatccaccc 240 acttcggctt cccaaagcat tgggagtata ggtgtgagcc actatacccg tcctcacatc 300 atatttctaa tcccgagact gtagagctgg tgtctctttt tctaaaggat gtcagtagag 360 aagtggagtt ccccaaaatt acagtttcac gtattagtca agtttctaaa atacagtaat 420 aatgttgaga gctgacatag ggactaactt ggtttttttt tttttttttt tttttcaaat 480 tctcactgaa ctttgatttt gctaaataag gacattaaaa aaaaaaccaa aaaactccac 540 tattgcctat tgccactatt tgatttttta aaaaataagc gtattttagc atctaaaagt 600 aggaaggacc tcaaataaat gagtctttgt tcttggccag ggaaaacagc gttgtcagaa 660 tttgataact gtttttctag ggtatgtgct gttattcagt taaaaccttg cctgggacgc 720 tagcattcag taaatacttg ttgaataagc aaatgaaact taagcttcta tgtatagaaa 780 cctaagtcac ttcacattct gattagcaga gtaattgaat attcttttca atgtgtagct 840 ctatccccag aaccacagaa tattggaact gtaaaggcca tcctatagtt taaccaactg 900 cgttaaatag ataatagaaa gatgtggtat gtggcagtga caacttgaag gttgtgacta 960 gaactcgggt ctctggagtg ttctattata tcacaccaag ctggtcacca gcccatgtgt 1020 tgatcctcca ttgtgatagc aacaaagaaa agacttcagg acattctttc ctttacccta 1080 atccttgatc tgcagtctta tttagaaaag cttaatgtta aagatctagt ttattcaaaa 1140 ctaaagataa caaggagtat gagaatttct atttcggagt gtaaaggagg agatgtttcc 1200 ttggcttctc tgagcctgca ggccttcctt gctctttaag gaagtagaga gagggaggaa 1260 agtaaagtat gcttttgttt tttaaggtta ctttgctggg agtagtttgc atgccttttg 1320 gttttcttgg gtggaattaa ctgacttaag ttttaagtag ttgggactat ttaaaaacaa 1380 tgcctatcca atgtttgcca taaaggcaga gggtattggc tttagaagtt aattcttctc 1440 caggagtgaa aattagcttc taaaccagaa gcagcagagc taaataaagt aattttccac 1500 ctggccagtg catgatgtga aaggtagatt aaaaaaatga gagggcccat tttctgatga 1560 aagactaagc catgttgaaa cagccctgtt gaggatttta ttttaaatct atacattcac 1620 aaaggagctt tgtgtatgtc tttccctatt tgttgtttgg actaggaagc cccacccagt 1680 gcttgttgaa ggcagaaagt cgttgaaagc aagctgggat ttgaacagtg gattgaggtt 1740 tcgaatatcc agtgaaccaa aatatatcag ggttcccctg gccaagatga gtgaccattc 1800 tgaggtgtta agtatttctt gaatggggat tttaggaaaa gtttctgtat ttctgtgctc 1860 attttgttga cctctgtatg tgcaaaatct ctaagggggt gtttgggcac ttagatttct 1920 tggatgcaga tttgtttgta tatgaaacaa attttaaatt gttttgtata cactggattt 1980 aaaatagttt actaaagtgt tttaattttt tcatcttaat tttcacagtt cttatagtct 2040 ttagatttag ggaggctgtt gatggcatcc acatgtgcat tttagtggca tttaaaatgt 2100 attcagctga atttaacaat ttctgaccta aaacttgaca ttttagattt aagtcggtaa 2160 agcactgatt taaactggat tttaactgga tgaaattctg atttaataag tgtactgact 2220 ggataaaatg ccaatgattt aattaacaag cacgtttaac aggatgccct atatattagt 2280 taaaagtgaa gcaattgaat taggtacctt ctctgctgcg tggaaaagac cgtatgactc 2340 acccacacca gccttctctt cgctctgagt gtagctaacc gtttctgttt tttttcctct 2400 agggtttgga aatcccttgt ctccaggttg ctgggattga cttcttgctc aattgaaaca 2460 ctcattcaat ggagacaaag agaactaatg ctttgtgctg attcatattt gaatcgaggc 2520 attgggaacc ctgtatgcct tgtttgtgga aagaaccagt gacaccatca ctgagcttcc 2580 taaaagttcg aagaagttag aggactatac actttctttt gaacttttat aataaatatt 2640 tgctctggtt tttggaaccc agggctgtta gaggggtgag tgacaagtct tacaagtggc 2700 cttattccaa ctccagaaat tgcccaacgg aactttgaga ttatatgcaa tcgaaagtga 2760 caggaaacat gccaactcaa tccctcttaa tgtacatgga tgggccagaa gtgattggca 2820 gctctcttgg cagtccgatg gagatggagg atgccttgtc aatgaaaggg accgctgttg 2880 ttccattccg agctacacaa gaaaaaaatg tcatccaaat cgaggggtat atgcccttgg 2940 attgcatgtt ctgcagccag accttcacac attcagaaga ccttaataaa catgtcttaa 3000 tgcaacaccg gcctaccctc tgtgaaccag cagttcttcg ggttgaagca gagtatctca 3060 gtccgcttga taaaagtcaa gtgcgaacag aacctcccaa ggaaaagaat tgcaaggaaa 3120 atgaatttag ctgtgaggta tgtgggcaga catttagagt cgcttttgat gttgagatcc 3180 acatgagaac acacaaagat tctttcactt acgggtgtaa catgtgcgga agaagattca 3240 aggagccttg gtttcttaaa aatcacatgc ggacacataa tggcaaatcg ggggccagaa 3300 gcaaactgca gcaaggcttg gagagtagtc cagcaacgat caacgaggtc gtccaggtgc 3360 acgcggccga gagcatctcc tctccttaca aaatctgcat ggtttgtggc ttcctatttc 3420 caaataaaga aagtctaatt gagcaccgca aggtgcacac caaaaaaact gctttcggta 3480 ccagcagcgc gcagacagac tctccacaag gaggaatgcc gtcctcgagg gaggacttcc 3540 tgcagttgtt caacttgaga ccaaaatctc accctgaaac ggggaagaag cctgtcagat 3600 gcatccctca gctcgatccg ttcaccacct tccaggcttg gcagctggct accaaaggaa 3660 aagttgccat ttgccaagaa gtgaaggaat cggggcaaga agggagcacc gacaacgacg 3720 attcgagttc cgagaaggag cttggagaaa caaataaggg cagttgtgca ggcctctcgc 3780 aagagaaaga gaagtgcaaa cactcccacg gcgaagcgcc ctccgtggac gcggatccca 3840 agttacccag tagcaaggag aagcccactc actgctccga gtgcggcaaa gctttcagaa 3900 cctaccacca gctggtcttg cactccaggg tccacaagaa ggaccggagg gccggcgcgg 3960 agtcgcccac catgtctgtg gacgggaggc agccggggac gtgttctcct gacctcgccg 4020 cccctctgga tgaaaatgga gccgtggatc gaggggaagg tggttctgaa gacggatctg 4080 aggatgggct tcccgaagga atccatctgg gtaagctgcc ctgtctccgt cccgtgctgt 4140 tccgcctgtg tctgtctgtc tccccgtctc cccctctcta ttcccatctc cagacaacgc 4200 tggccaggaa tggggtttgg agagccagag tcaagtccag gctctttttg gtatcactct 4260 gtgtaagtca tttaacctct cagggcctta attttctcat ttctgtaata acagggttga 4320 gttaagaggt ctccttgttc tgaaaatata tatatatttt ttaaacgtgt atcgttttgc 4380 tcacaaaaca cactttaaaa aaaaaataac ttgtgcatcc agcccaaatg cactgcttct 4440 taactggggc gattttgttc ccaatcagta tctggcaatg tctggaggca ttttggttgt 4500 catactgtgt gtgtgggtgt gcctgctggc atccagtggg cagaggccag ggacactgct 4560 cagcatggta cagtgcacag gacagcccca tcatcaaaga attatctggt cccaaatgtc 4620 aatagtttga gcattgagag accctagcct tcacttaagt ttttctggcg ttcctgatct 4680 ttttctgtag tgaatttcta gtggccataa aaggtactgg gagtgatcaa ctagagccag 4740 gaatattatt tgggcagccg tttggtgctg tccaaaacct tgtcctttct gtctggcaag 4800 ctagtatcca tttataggta cctcaggaac ccaaatgatt tgtcataaaa tacaaggaat 4860 gtgagcacac tgaagacatt tttaagaagg ctcatttgct cagcagaatt ttcagtgtac 4920 tagtggcatt tatagaaaga gaaggtgatc actgaaggca tgctcacata atattcctga 4980 gccctggtgg gcgttatcta gggcaaagga ttccacctgt gtttggagtt gcgcccatcc 5040 tcactgtagc cagagcttct cctatcagag tttagtattt tgtttgaata gaggatcttg 5100 ctgcttaaaa cagttgaaaa gaccctgatg ggcaggccgt aattgacaag cgaatgatgg 5160 gaacatgaat cggtcttagg gaagcatctg tcaaagtggt ccttggttaa aacaagtgcc 5220 tcctcctctc agtgtcactt gattgtgtgc ttgaattctt cggaaaactg ggtgtatgag 5280 acccacgatg aatttgccca cacgattgat tggactcttc cttcacctgc tcttcagcca 5340 gtgccagttc cttttctgat catgtgattg acgtgagaac tgtagtctgt atatcaaatc 5400 tttagaatgt ttttgagttt cctgggacac aggaaaccca gcacttagca tactacaaat 5460 ctaatgtctt aatggcatca taaaaagagg ctttaaacac agactccagt tagctaagtg 5520 gtttctgcta gtgccggtac tgttgcaggg gccctgtgag atgccccagt tccctgaaag 5580 aaatgaaaag gccagttacc ggtaggtggt gtggaaaaca tgggctagat catcaggcag 5640 gacagaatgc ctggctgtgg gtgggagcac cccagcttgg cgttgagttc tggttctacc 5700 actgcgttgt tttgtgacca attatgagtt gcttaacctt tctttgctac tatttccctg 5760 tttgcaaaat ggttcattga cccctgtctt ccacctccca aggacaattt caacagccta 5820 tttgtaaaaa gatcacagtc ctttaaaaaa tataactgta aagtcagagg tgatgcttga 5880 aagagcagga accaggtaga tgtggaaatg tcatgtcctt tgttctaaag aaaaggcatt 5940 tcatagcttt ttggatatga cgcaacatac cataaatcct gacacatagt tgggagtcgg 6000 aaattgcaac aacgcccagt tataaaccca gctagtttgg gtatgattgt aagaaaaaaa 6060 agctggccat tctgtatttg gggaattgat tttcctaaac ttatattatc ttagtagtct 6120 agatttatca tattgtacta tcatcctggc ttttttaaga cttaagaaga tcaagtaaat 6180 ttttttttct ttctttagac actatataga tcatcaaggg tgtctgtctt acaggtggat 6240 agtgatatga tctacagtga ggggacattt atttaaaact taaacattca tgtgttttgg 6300 gggtggtatt ttaacggcag cacctctgat tgtcttttgg agggctggtg tgtgtttgaa 6360 gttctgtcct ccttccagtg gactctaact tctcctgatg cacgtgagac acattgtcct 6420 attgtcctgc agaaactaaa gccaaacact gtcatctggg gacaggtttt catttgtcag 6480 atctctttcg cccacatgag tgtttgtgga caatacagcc tgctttccaa aactttgcta 6540 aattttgaca gactttccta ggtgcttgcc caatgccaga ctttcttttc tgttgaagat 6600 taagttgtgc ttgctgccct ctagtggtca gttgtttaat cctaacctta aacggcttat 6660 ttttcccctg gtggttggga agttgacggt ttgtaattgg ctcatttttc taaattattc 6720 tgaagaagat aatttttccc gccagtatgt atgtccacct tcagtttgcc agatcctgcc 6780 tgctcagaga cactgagaac cggaagctgc ccgggcaatt cagtctatga aatgatcttt 6840 cttgtgatta aggcaaacga agaactgaat gtttaatagt gtactctgct gtacccagaa 6900 aaaaacaaaa caaaatcatg ttataacact ctaaaacttc aaacaacctc caacagcatt 6960 tggtgtgtgt ctagccgttt tgttctaacc cgatgttata taaaagaatt ttttcatgct 7020 ttccaaaaat gtttatgtca agaatattta agtcagcatg ccttattcag gtacttcagc 7080 taccttctta tataaatatt tttgtttttc ctttaagata aaaatgatga tggaggaaaa 7140 ataaaacatc ttacatcttc aagagagtgt agttattgtg gaaagttttt ccgttcaaat 7200 tattacctca atattcatct cagaacgcat acaggtaaag aacttttatt tttttaacca 7260 tgcattagtt aaattatgta gttatctaat ttttttgttg ttgttgttca gatactctgc 7320 cagatccttg gactagctta aggataaata tgtagcatgt tgattgcagt ggttattttt 7380 attcttttag tgccattgta acttgagcca ttgttcttat ttgcagttca tttcttttct 7440 ttcttttttg ttttttgaga cggagtcttg ctctgtcacc tcggctggag tgcagtggtg 7500 caatttcggc tcactgcagc ctccacctcc ctggttcaag caatactcct gcctcagcct 7560 ccccagtagt tgggattaca ggtacctgcc accacacccg gctaatttct gtatttttag 7620 tagagatggg gtttcaccat gctggccagg ctggtttcga actcctgacc tcaagtgatc 7680 cgctcacctt ggcctcccat agtgttggcc tcccatagtg ctgggattac aggcgtgagc 7740 caccgcgccc ggacaaagtt catttgttta gtttatgact gctatgtcct gactcttatc 7800 ttattaaaag ctacagtatt ttaaaatgct gcatcttatg tctttatgat tgagaatgaa 7860 atgagaatct atttagtagt cttgagattg tgaaaggagc tatgacatca tgatgtagga 7920 ggctgcgtag atttgaaatt tcatctcttc cacttactat ctgtgcaccc ttgggcaagt 7980 tatttaacct ttttgtgctt ttagttttct ttgctgtaaa agtagaataa tacatatttc 8040 cctagggctg ttaggaagat taaataagtt agaagtgttg ctgttaattt ttctattgaa 8100 gataggcatt cataatttca aatattcatt acagtaagga tgataaagaa ctgatgagaa 8160 atcctatgtg atagtagatc gagaaagcaa aaggaggaaa gaagcctgtt ttcttaataa 8220 atagatattt gatctatttc agtgcttttc atacacttct ataataaagt gccatttctt 8280 gccttaggtg aaaaaccata caaatgtgaa ttttgtgaat atgctgcagc ccagaagaca 8340 tctctgaggt atcacttgga gagacatcac aaggaaaaac aaaccgatgt tgctgctgaa 8400 gtcaagaacg atggtaaaaa tcaggacact gaagatgcac tattaaccgc tgacagtgcg 8460 caaaccaaaa atttgaaaag attttttgat ggtgccaaag atgttacagg cagtccacct 8520 gcaaagcagc ttaaggagat gccttctgtt tttcagaatg ttctgggcag cgctgtcctc 8580 tcaccagcac acaaagatac tcaggatttc cataaaaatg cagctgatga cagtgctgat 8640 aaagtgaata aaaaccctac ccctgcttac ctggacctgt taaaaaagag atcagcagtt 8700 gaaactcagg caaataacct catctgtaga accaaggcgg atgttactcc tcctccggat 8760 ggcagtacca cccataacct tgaagttagc cccaaagaga agcaaacgga gaccgcagct 8820 gactgcagat acaggccaag tgtggattgt cacgaaaaac ctttaaattt atccgtgggg 8880 gctcttcaca attgcccggc aatttctttg agtaaaagtt tgattccaag tatcacctgt 8940 ccattttgta ccttcaagac attttatcca gaagttttaa tgatgcacca gagactggag 9000 cataaataca atcctgacgt tcataaaaac tgtcgaaaca agtccttgct tagaagtcga 9060 cgtaccggat gcccgccagc gttgctggga aaagatgtgc ctcccctccc tagtttctgt 9120 aaacccaagc ccaagtctgc tttcccggcg cagtccaaat ccctgccatc tgcgaagggg 9180 aagcagagcc ctcctgggcc aggcaaggcc cctctgactt cagggataga ctctagcact 9240 ttagccccaa gtaacctgaa gtcccacaga ccacagcaga atgtgggggt ccaaggggcc 9300 gccaccaggc aacagcaatc tgagatgttt cctaaaacca gtgtttcccc tgcaccggat 9360 aagacaaaaa gacccgagac aaaattgaaa cctcttccag tagctccttc tcagcccacc 9420 ctcggcagca gtaacatcaa tggttccatc gactaccccg ccaagaacga cagcccgtgg 9480 gcacctccgg gaagagacta tttctgtaat cggagtgcca gcaatactgc agcagaattt 9540 ggtgagcccc ttccaaaaag actgaagtcc agcgtggttg cccttgacgt tgaccagccc 9600 ggggccaatt acagaagagg ctatgacctt cccaagtacc atatggtcag aggcatcaca 9660 tcactgttac cgcaggactg tgtgtatccg tcgcaggcgc tgcctcccaa accaaggttc 9720 ctgagctcca gcgaggtcga ttctccaaat gtgctgactg ttcagaagcc ctatggtggc 9780 tccgggccac tttacacttg tgtgcctgct ggtagtccag catccagctc gacgttagaa 9840 ggtattgcat gaggggcgtc gtgtttaaat ggctgcctac agtgattaat agctaatcca 9900 ggcattctca gtggagatgg taccactccc aagggtgggg ggtaggcagc cagaagttct 9960 tgggggtcac agagagaagc attcttagat acggcagtgg tttgtggtcc tccaaggctt 10020 acttaactct gtgggtttaa ctcttaaccc tgtgtatttt attcttttga tttgtttagt 10080 cttactttat ttttagagaa agggtcttgc tccgtcatct agattggagt gcagcggtgt 10140 aatcatagct tactgtagtc ttgaattcct gagttcaaga gatccttctg cctcagcttc 10200 ccaggtagct gagactatat gtgctgctac catgcacagc tgatttttaa attttttttg 10260 tagagatgga gttgcccagg ctggtcttga actcctggcc tgaggtgatc ctcctgcgtt 10320 gacctcccaa gtatcttaga ctacagatgc actccaccac gcttg 10365 10 3186 DNA Artificial Sequence Description of Artificial SequenceZABC1 Open Reading Frame 10 atgcaatcga aagtgacagg aaacatgcca actcaatccc tcttaatgta catggatggg 60 ccagaagtga ttggcagctc tcttggcagt ccgatggaga tggaggatgc cttgtcaatg 120 aaagggaccg ctgttgttcc attccgagct acacaagaaa aaaatgtcat ccaaatcgag 180 gggtatatgc ccttggattg catgttctgc agccagacct tcacacattc agaagacctt 240 aataaacatg tcttaatgca acaccggcct accctctgtg aaccagcagt tcttcgggtt 300 gaagcagagt atctcagtcc gcttgataaa agtcaagtgc gaacagaacc tcccaaggaa 360 aagaattgca aggaaaatga atttagctgt gaggtatgtg ggcagacatt tagagtcgct 420 tttgatgttg agatccacat gagaacacac aaagattctt tcacttacgg gtgtaacatg 480 tgcggaagaa gattcaagga gccttggttt cttaaaaatc acatgcggac acataatggc 540 aaatcggggg ccagaagcaa actgcagcaa ggcttggaga gtagtccagc aacgatcaac 600 gaggtcgtcc aggtgcacgc ggccgagagc atctcctctc cttacaaaat ctgcatggtt 660 tgtggcttcc tatttccaaa taaagaaagt ctaattgagc accgcaaggt gcacaccaaa 720 aaaactgctt tcggtaccag cagcgcgcag acagactctc cacaaggagg aatgccgtcc 780 tcgagggagg acttcctgca gttgttcaac ttgagaccaa aatctcaccc tgaaacgggg 840 aagaagcctg tcagatgcat ccctcagctc gatccgttca ccaccttcca ggcttggcag 900 ctggctacca aaggaaaagt tgccatttgc caagaagtga aggaatcggg gcaagaaggg 960 agcaccgaca acgacgattc gagttccgag aaggagcttg gagaaacaaa taagggcagt 1020 tgtgcaggcc tctcgcaaga gaaagagaag tgcaaacact cccacggcga agcgccctcc 1080 gtggacgcgg atcccaagtt acccagtagc aaggagaagc ccactcactg ctccgagtgc 1140 ggcaaagctt tcagaaccta ccaccagctg gtcttgcact ccagggtcca caagaaggac 1200 cggagggccg gcgcggagtc gcccaccatg tctgtggacg ggaggcagcc ggggacgtgt 1260 tctcctgacc tcgccgcccc tctggatgaa aatggagccg tggatcgagg ggaaggtggt 1320 tctgaagacg gatctgagga tgggcttccc gaaggaatcc atctggataa aaatgatgat 1380 ggaggaaaaa taaaacatct tacatcttca agagagtgta gttattgtgg aaagtttttc 1440 cgttcaaatt attacctcaa tattcatctc agaacgcata caggtgaaaa accatacaaa 1500 tgtgaatttt gtgaatatgc tgcagcccag aagacatctc tgaggtatca cttggagaga 1560 catcacaagg aaaaacaaac cgatgttgct gctgaagtca agaacgatgg taaaaatcag 1620 gacactgaag atgcactatt aaccgctgac agtgcgcaaa ccaaaaattt gaaaagattt 1680 tttgatggtg ccaaagatgt tacaggcagt ccacctgcaa agcagcttaa ggagatgcct 1740 tctgtttttc agaatgttct gggcagcgct gtcctctcac cagcacacaa agatactcag 1800 gatttccata aaaatgcagc tgatgacagt gctgataaag tgaataaaaa ccctacccct 1860 gcttacctgg acctgttaaa aaagagatca gcagttgaaa ctcaggcaaa taacctcatc 1920 tgtagaacca aggcggatgt tactcctcct ccggatggca gtaccaccca taaccttgaa 1980 gttagcccca aagagaagca aacggagacc gcagctgact gcagatacag gccaagtgtg 2040 gattgtcacg aaaaaccttt aaatttatcc gtgggggctc ttcacaattg cccggcaatt 2100 tctttgagta aaagtttgat tccaagtatc acctgtccat tttgtacctt caagacattt 2160 tatccagaag ttttaatgat gcaccagaga ctggagcata aatacaatcc tgacgttcat 2220 aaaaactgtc gaaacaagtc cttgcttaga agtcgacgta ccggatgccc gccagcgttg 2280 ctgggaaaag atgtgcctcc cctctctagt ttctgtaaac ccaagcccaa gtctgctttc 2340 ccggcgcagt ccaaatccct gccatctgcg aaggggaagc agagccctcc tgggccaggc 2400 aaggcccctc tgacttcagg gatagactct agcactttag ccccaagtaa cctgaagtcc 2460 cacagaccac agcagaatgt gggggtccaa ggggccgcca ccaggcaaca gcaatctgag 2520 atgtttccta aaaccagtgt ttcccctgca ccggataaga caaaaagacc cgagacaaaa 2580 ttgaaacctc ttccagtagc tccttctcag cccaccctcg gcagcagtaa catcaatggt 2640 tccatcgact accccgccaa gaacgacagc ccgtgggcac ctccgggaag agactatttc 2700 tgtaatcgga gtgccagcaa tactgcagca gaatttggtg agccccttcc aaaaagactg 2760 aagtccagcg tggttgccct tgacgttgac cagcccgggg ccaattacag aagaggctat 2820 gaccttccca agtaccatat ggtcagaggc atcacatcac tgttaccgca ggactgtgtg 2880 tatccgtcgc aggcgctgcc tcccaaacca aggttcctga gctccagcga ggtcgattct 2940 ccaaatgtgc tgactgttca gaagccctat ggtggctccg ggccacttta cacttgtgtg 3000 cctgctggta gtccagcatc cagctcgacg ttagaaggtc ttggtggatg tcagtgctta 3060 ctccccatga aattaaattt tacttcatcc tttgagaagc gaatggtgaa agctactgaa 3120 ataagctgtg attgtactgt acataaaaca tatgaggaat ctgcaaggaa cactacagtt 3180 gtgtaa 3186 11 1061 PRT Artificial Sequence Description of Artificial SequenceZABC1 Protein 11 Met Gln Ser Lys Val Thr Gly Asn Met Pro Thr Gln Ser Leu Leu Met 1 5 10 15 Tyr Met Asp Gly Pro Glu Val Ile Gly Ser Ser Leu Gly Ser Pro Met 20 25 30 Glu Met Glu Asp Ala Leu Ser Met Lys Gly Thr Ala Val Val Pro Phe 35 40 45 Arg Ala Thr Gln Glu Lys Asn Val Ile Gln Ile Glu Gly Tyr Met Pro 50 55 60 Leu Asp Cys Met Phe Cys Ser Gln Thr Phe Thr His Ser Glu Asp Leu 65 70 75 80 Asn Lys His Val Leu Met Gln His Arg Pro Thr Leu Cys Glu Pro Ala 85 90 95 Val Leu Arg Val Glu Ala Glu Tyr Leu Ser Pro Leu Asp Lys Ser Gln 100 105 110 Val Arg Thr Glu Pro Pro Lys Glu Lys Asn Cys Lys Glu Asn Glu Phe 115 120 125 Ser Cys Glu Val Cys Gly Gln Thr Phe Arg Val Ala Phe Asp Val Glu 130 135 140 Ile His Met Arg Thr His Lys Asp Ser Phe Thr Tyr Gly Cys Asn Met 145 150 155 160 Cys Gly Arg Arg Arg Lys Glu Pro Trp Phe Leu Lys Asn His Met Arg 165 170 175 Thr His Asn Gly Lys Ser Gly Ala Arg Ser Lys Leu Gln Gln Gly Leu 180 185 190 Glu Ser Ser Pro Ala Thr Ile Asn Glu Val Val Gln Val His Ala Ala 195 200 205 Glu Ser Ile Ser Ser Pro Tyr Lys Ile Cys Met Val Cys Gly Phe Leu 210 215 220 Phe Pro Asn Lys Glu Ser Leu Ile Glu His Arg Lys Val His Thr Lys 225 230 235 240 Lys Thr Ala Phe Gly Thr Ser Ser Ala Gln Thr Asp Ser Pro Gln Gly 245 250 255 Gly Met Pro Ser Ser Arg Glu Asp Phe Leu Gln Leu Phe Asn Leu Arg 260 265 270 Pro Lys Ser His Pro Glu Thr Gly Lys Lys Pro Val Arg Cys Ile Pro 275 280 285 Gln Leu Asp Pro Phe Thr Thr Phe Gln Ala Trp Gln Leu Ala Thr Lys 290 295 300 Gly Lys Val Ala Ile Cys Gln Glu Val Lys Glu Ser Gly Gln Glu Gly 305 310 315 320 Ser Thr Asp Asn Asp Asp Ser Ser Ser Glu Lys Glu Leu Gly Glu Thr 325 330 335 Asn Lys Gly Ser Cys Ala Gly Leu Ser Gln Glu Lys Glu Lys Cys Lys 340 345 350 His Ser His Gly Glu Ala Pro Ser Val Asp Ala Asp Pro Lys Leu Pro 355 360 365 Ser Ser Lys Glu Lys Pro Thr His Cys Ser Glu Cys Gly Lys Ala Phe 370 375 380 Arg Thr Tyr His Gln Leu Val Leu His Ser Arg Val His Lys Lys Asp 385 390 395 400 Arg Arg Ala Gly Ala Glu Ser Pro Thr Met Ser Val Asp Gly Arg Gln 405 410 415 Pro Gly Thr Cys Ser Pro Asp Leu Ala Ala Pro Leu Asp Glu Asn Gly 420 425 430 Ala Val Asp Arg Gly Glu Gly Gly Ser Glu Asp Gly Ser Glu Asp Gly 435 440 445 Leu Pro Glu Gly Ile His Leu Asp Lys Asn Asp Asp Gly Gly Lys Ile 450 455 460 Lys His Leu Thr Ser Ser Arg Glu Cys Ser Tyr Cys Gly Lys Phe Phe 465 470 475 480 Arg Ser Asn Tyr Tyr Leu Asn Ile His Leu Arg Thr His Thr Gly Glu 485 490 495 Lys Pro Tyr Lys Cys Glu Phe Cys Glu Tyr Ala Ala Ala Gln Lys Thr 500 505 510 Ser Leu Arg Tyr His Leu Glu Arg His His Lys Glu Lys Gln Thr Asp 515 520 525 Val Ala Ala Glu Val Lys Asn Asp Gly Lys Asn Gln Asp Thr Glu Asp 530 535 540 Ala Leu Leu Thr Ala Asp Ser Ala Gln Thr Lys Asn Leu Lys Arg Phe 545 550 555 560 Phe Asp Gly Ala Lys Asp Val Thr Gly Ser Pro Pro Ala Lys Gln Leu 565 570 575 Lys Glu Met Pro Ser Val Phe Gln Asn Val Leu Gly Ser Ala Val Leu 580 585 590 Ser Pro Ala His Lys Asp Thr Gln Asp Phe His Lys Asn Ala Ala Asp 595 600 605 Asp Ser Ala Asp Lys Val Asn Lys Asn Pro Thr Pro Ala Tyr Leu Asp 610 615 620 Leu Leu Lys Lys Arg Ser Ala Val Glu Thr Gln Ala Asn Asn Leu Ile 625 630 635 640 Cys Arg Thr Lys Ala Asp Val Thr Pro Pro Pro Asp Gly Ser Thr Thr 645 650 655 His Asn Leu Glu Val Ser Pro Lys Glu Lys Gln Thr Glu Thr Ala Ala 660 665 670 Asp Cys Arg Tyr Arg Pro Ser Val Asp Cys His Glu Lys Pro Leu Asn 675 680 685 Leu Ser Val Gly Ala Leu His Asn Cys Pro Ala Ile Ser Leu Ser Lys 690 695 700 Ser Leu Ile Pro Ser Ile Thr Cys Pro Phe Cys Thr Phe Lys Thr Phe 705 710 715 720 Tyr Pro Glu Val Leu Met Met His Gln Arg Leu Glu His Lys Tyr Asn 725 730 735 Pro Asp Val His Lys Asn Cys Arg Asn Lys Ser Leu Leu Arg Ser Arg 740 745 750 Arg Thr Gly Cys Pro Pro Ala Leu Leu Gly Lys Asp Val Pro Pro Leu 755 760 765 Ser Ser Phe Cys Lys Pro Lys Pro Lys Ser Ala Phe Pro Ala Gln Ser 770 775 780 Lys Ser Leu Pro Ser Ala Lys Gly Lys Gln Ser Pro Pro Gly Pro Gly 785 790 795 800 Lys Ala Pro Leu Thr Ser Gly Ile Asp Ser Ser Thr Leu Ala Pro Ser 805 810 815 Asn Leu Lys Ser His Arg Pro Gln Gln Asn Val Gly Val Gln Gly Ala 820 825 830 Ala Thr Arg Gln Gln Gln Ser Glu Met Phe Pro Lys Thr Ser Val Ser 835 840 845 Pro Ala Pro Asp Lys Thr Lys Arg Pro Glu Thr Lys Leu Lys Pro Leu 850 855 860 Pro Val Ala Pro Ser Gln Pro Thr Leu Gly Ser Ser Asn Ile Asn Gly 865 870 875 880 Ser Ile Asp Tyr Pro Ala Lys Asn Asp Ser Pro Trp Ala Pro Pro Gly 885 890 895 Arg Asp Tyr Phe Cys Asn Arg Ser Ala Ser Asn Thr Ala Ala Glu Phe 900 905 910 Gly Glu Pro Leu Pro Lys Arg Leu Lys Ser Ser Val Val Ala Leu Asp 915 920 925 Val Asp Gln Pro Gly Ala Asn Tyr Arg Arg Gly Tyr Asp Leu Pro Lys 930 935 940 Tyr His Met Val Arg Gly Ile Thr Ser Leu Leu Pro Gln Asp Cys Val 945 950 955 960 Tyr Pro Ser Gln Ala Leu Pro Pro Lys Pro Arg Phe Leu Ser Ser Ser 965 970 975 Glu Val Asp Ser Pro Asn Val Leu Thr Val Gln Lys Pro Tyr Gly Gly 980 985 990 Ser Gly Pro Leu Tyr Thr Cys Val Pro Ala Gly Ser Pro Ala Ser Ser 995 1000 1005 Ser Thr Leu Glu Gly Leu Gly Gly Cys Gln Cys Leu Leu Pro Met Lys 1010 1015 1020 Leu Asn Phe Thr Ser Ser Phe Glu Lys Arg Met Val Lys Ala Thr Glu 1025 1030 1035 1040 Ile Ser Cys Asp Cys Thr Val His Lys Thr Tyr Glu Glu Ser Ala Arg 1045 1050 1055 Asn Thr Thr Val Val 1060 12 3066 DNA Artificial Sequence Description of Artificial Sequence1b1 12 ggaaacagct atgaccatga ttacgccaag ctcgaaatta accctcacta aagggaacaa 60 aagctggagc tccaccgcgg tggcggccgc tctagaacta gtggatcccc cgggctgcag 120 gaattcggca cgaggctcca ccgacagcca ggcactgggc agcacgcact ggagacccag 180 gaccctgtgc aggagcagct ccgggtgaca cgaggggact gaagatactc ccacaggggc 240 tcagcaggag caatgggtaa ccaaatgagt gttccccaaa gagttgaaga ccaagagaat 300 gaaccagaag cagagactta ccaggacaac gcgtctgctc tgaacggggt tccagtggtg 360 gtgtcgaccc acacagttca gcacttagag gaagtcgact tgggaataag tgtcaagacg 420 gataatgtgg ccacttcttc ccccgagaca acggagataa gtgctgttgc ggatgccaac 480 ggaaagaatc ttgggaaaga ggccaaaccc gaggcaccag ctgctaaatc tcgttttttc 540 ttgatgctct ctcggcctgt accaggacgt accggagacc aagccgcaga ttcatccctt 600 ggatcagtga agcttgatgt cagctccaat aaagctccag cgaacaaaga cccaagtgag 660 agctggacac ttccggtggc agctggaccg gggcaggaca cagataaaac cccagggcac 720 gccccggccc aagacaaggt cctctctgcc gccagggatc ccacgcttct cccacctgag 780 acagggggag caggaggaga agctccctcc aagcccaagg actccagctt ttttgacaaa 840 ttcttcaagc tggacaaggg acaggaaaag gtgccaggtg acagccaaca ggaagccaag 900 agggcagagc atcaagacaa ggtggatgag gttcctggct tatcagggca gtccgatgat 960 gtccctgcag ggaaggacat agttgacggc aaggaaaaag aaggacaaga acttggaact 1020 gcggattgct ctgtccctgg ggacccagaa ggactggaga ctgcaaagga cgattcccag 1080 gcagcagcta tagcagagaa taataattcc atcatgagtt tctttaaaac tctggtttca 1140 cctaacaaag ctgaaacaaa aaaggaccca gaagacacgg gtgctgaaaa gtcacccacc 1200 acttcagctg accttaagtc agacaaagcc aactttacat cccaggagac ccaaggggct 1260 ggcaagaatt ccaaaggatg caacccatcg gggcacacac agtccgtgac aacccctgaa 1320 cctgcgaagg aaggcaccaa ggagaaatca ggacccacct ctctgcctct gggcaaactg 1380 ttttggaaaa agtcagttaa agaggactca gtccccacag gtgcggagga gaatgtggtg 1440 tgtgagtcac cagtagagat tataaagtcc aaggaagtag aatcagcctt acaaacagtg 1500 gacctcaacg aaggagatgc tgcacctgaa cccacagaag cgaaactcaa aagagaagaa 1560 agcaaaccaa gaacctctct gatggcgttt ctcagacaaa tgtcagtgaa aggggatgga 1620 gggatcaccc actcagaaga aataaatggg aaagactcca gctgccaaac atcagactcc 1680 acagaaaaga ctatcacacc gccagagcct gaaccaacag gagcaccaca gaagggtaaa 1740 gagggctcct cgaaggacaa gaagtcagca gccgagatga acaagcagaa gagcaacaag 1800 caggaagcca aagaaccagc ccagtgcaca gagcaggcca cggtggacac gaactcactg 1860 cagaatgggg acaagctcca aaagagacct gagaagcggc agcagtccct tgggggcttc 1920 tttaaaggcc tgggaccaaa gcggatgttg gatgctcaag tgcaaacaga cccagtatcc 1980 atcggaccag ttggcaaacc caagtaaaca aatcagcacg gttcccacca ggttctcctg 2040 ccaccaagat gtgttctcct tactccatct cctccccaaa cacgctccat gtatatattc 2100 ttctgatggc cagcaaatga aattctgcct agaaattaag cccgagctgt tgtatattga 2160 ggtgtattat ttacgtctct ggtccagtct tttctggcaa ataacagtaa agatggttta 2220 gcaggtcacc tagttgggtc agaagagtcg atgatcacca agcaggaaag ggagggaata 2280 gaggaatgtg ttcgggttaa gtgatgaaaa tggcagtggt ggccgggcgt ggtggctctc 2340 gcctgtaatc tcagcacttt gggaggccga ggcaggtgga tcacctgagg tcaggagttc 2400 aagactagcc tggccaacat catgaaaccc cgtctctact aaaaatacaa aaattagcca 2460 ggcatggtgg cacacacctg tagtcccagc tactcgggag cccaacgcac gagaaccgct 2520 tgtacccagg aggtggaggt tgcagtgagc cgaagttgca ccattgcact ccaccctggg 2580 cgacagagca agattctatc aaaaaaaaaa ggcagtggca agtaagttat agaagagaaa 2640 tgctgctaga aggaattaag cgttgtagta aacgcgtgct catcctctaa gcttgaagaa 2700 gggagacgaa aatccatttg tttaaattca catctcaagg agggagaacc cgggctgtgt 2760 tgggtggttg ccaatttcct agaacggaat gtgtggggta tagaaaaagg aatgaataag 2820 cgttgttttt caaatagggt ccttgtaagt tattgatgag agggaaaaga ttgactgggg 2880 agggcttaaa atgatttggg aaaacaattg cttttgaggc tcagtgacaa cggcaaagat 2940 tacaacttaa aaaaaaaaaa aaaaaaactc gagactagtt ctctctctct ctcgtgccga 3000 attcgatatc aagcttatcg ataccgtcga cctcgagggg gggcccggta cccaattcgc 3060 cctata 3066 13 939 DNA Artificial Sequence Description of Artificial SequenceGenomic Sequence from BAC Clone 97 Filtered Query Sequence 13 tgtgatattg attcatgccc tcttgcacct tgccaaacat cacacgcttg ccatccagtc 60 cactcgattt tggcagtgca gatgaaaaac tgggaaccat ttgtgttgag tccagcaaga 120 tgccaggacc tgcatgtttc agaacgaagt tcttcatcat ccaatttctc cctgtatatg 180 ggcttaccac nactgccgtt aagtcgtgtn aagtcaccac tcaggtacat aatggaataa 240 ttctgcaaag gcaggagnca ctttctctcc agtgctcaga ccatgaaagt tttctgatgt 300 ctttggaact ttgtctgcaa atagctcgaa ggagacatgg cctaaaggct cgccatctgc 360 ggtgatattg naacatggta gggctgaccg tggctgtggc catgactttt tagantnnnn 420 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 480 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnncccaat gcgggacaga gaatcnaaga 540 aactgtatta gggaaagggt cctgagttta tgccaaagtt tcccagattg gtttccattg 600 aaacgtagct ctgtgagata ccatcaggtg ttatgtgaag aaatgtctgt gtagtcaaat 660 atgtttgagt gagtgagcct gagctgagca agactttact gcaagacttc ccatcttctg 720 tcccttttta tgctaatggg taacacaaac tccaaaagtg gggtgtacag catgaggcat 780 taacaaaaat ttattggacc ccacacacnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 840 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 900 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnctctc 939 14 112 DNA Artificial Sequence Description of Artificial SequenceSubject Seq - Rat Cyclophillin 64-175 14 ttcgacatca cggctgatgg cgagcccttg ggtcgcgtct gcttcgagct gtttgcagac 60 aaagttccaa agacagcaga aaactttcgt gctctgagca ctggggagaa ag 112 15 106 DNA Artificial Sequence Description of Artificial SequenceeSubject Seq - Rat Cyclophilli404-348 15 tgctggacca aacacaaatg gttcccagtt ttttatctgc actgccaaga ctgagtgggg 60 ctggatggca agcatgtggt ctttgggaag gtgaaagaag gcatga 106 16 38 DNA Artificial Sequence Description of Artificial SequenceeSubject Seq - Rat Cyclophillin 299-336 16 agaacttcat cctgaagcat acaggtcctg gcatcttg 38 17 28 DNA Artificial Sequence Description of Artificial SequenceeSubject Seq - Rat Cyclophillin 193-220 17 tcctcctttc acagaattat tccaggat 28 18 112 DNA Artificial Sequence Description of Artificial SequenceQuery Seq ID NO 13 261-372 18 tncaatatca ccgcagatgg cgagccttta ggccatgtct ccttcgagct atttgcagac 60 aaagttccaa agacatcaga aaactttcat ggtctgagca ctggagagaa ag 112 19 106 DNA Artificial Sequence Description of Artificial SequenceQuery Seq ID NO 13 13-117 19 tgctggactc aacacaaatg gttcccagtt tttcatctgc actgccaaaa tcgagtggga 60 ctggatggca agcgtgtgat gtttggcaag gtgcaagagg gcatga 106 20 38 DNA Artificial Sequence Description of Artificial SequenceQuery Seq ID NO 13116-153 20 agaacttcgt tctgaaacat gcaggtcctg gcatcttg 38 21 28 DNA Artificial Sequence Description of Artificial SequenceQuery Seq ID NO 13 229-256 21 tcctgccttt gcagaattat tccattat 28 22 23 DNA Artificial Sequence Description of Artificial Sequence Forward primer 22 ttggcattgg tatcaggtag ctg 23 23 24 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 23 ttggagcaga gaggggattg tgtg 24 24 24 DNA Artificial Sequence Description of Artificial Sequence:: Forward primer 24 aatcccctca aaccctgctg ctac 24 25 22 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 25 tggagcctga acttctgcaa tc 22 26 17 DNA Artificial Sequence Description of Artificial Sequence:: Forward primer 26 ccgggatacc gacattg 17 27 19 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 27 tgcacataaa acagccagc 19 28 20 DNA Artificial Sequence Description of Artificial Sequence:: Forward primer 28 ttggaatcaa tggagcaaaa 20 29 20 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 29 agctttaccc aatgtggtcc 20 30 21 DNA Artificial Sequence Description of Artificial Sequence:: Forward primer 30 gtggtgaaca ccaataaatg g 21 31 24 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 31 aagcaaataa aaccaataaa ctcg 24 32 21 DNA Artificial Sequence Description of Artificial Sequence:: Forward primer 32 caagatctga ccccgtcaat c 21 33 25 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 33 gacttcttca ggaaagagat cagtg 25 34 23 DNA Artificial Sequence Description of Artificial Sequence:: Forward primer 34 gccatgtacc cacctgaaaa atc 23 35 24 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 35 tcagaacacc cgtgcagaat taag 24 36 24 DNA Artificial Sequence Description of Artificial Sequence:: Forward primer 36 cctaaaactt ggtgcttaaa tcta 24 37 20 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 37 gtctcacaag gcagatgtgg 20 38 20 DNA Artificial Sequence Description of Artificial Sequence:: Forward primer 38 tttgtgtatg ttgagccatc 20 39 22 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 39 cttccaatct cattctatga gg 22 40 22 DNA Artificial Sequence Description of Artificial SequenceForward Primer 40 gcttgtttaa gtgtcactag gg 22 41 23 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 41 cactctggta aatgaccttt gtc 23 42 21 DNA Artificial Sequence Description of Artificial Sequence:: Forward primer 42 cctacaccat tccaactttg g 21 43 25 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 43 gccagatgta tgtttgctac ggaac 25 44 22 DNA Artificial Sequence Description of Artificial Sequence:: Forward primer 44 tctcaaacct gtccacttct tg 22 45 19 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 45 ctgctgtggt ggagaatgg 19 46 24 DNA Artificial Sequence Description of Artificial Sequence:: Forward primer 46 tgtcctcctt ctccctcatc ctac 24 47 22 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 47 aatgcctcca ctcacaggaa tg 22 48 23 DNA Artificial Sequence Description of Artificial Sequence:: Forward primer 48 cctcttcagt gtcttcctat tga 23 49 20 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 49 gggaggaggt tgtaggcaac 20 50 21 DNA Artificial Sequence Description of Artificial Sequence Forward primer 50 agcaaagcaa aggtggcaca c 21 51 24 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 51 tgacatggga gaagacacac ttcc 24 52 20 DNA Artificial Sequence Description of Artificial SequenceForward Primer 52 aggtttacca atgtgtttgg 20 53 21 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 53 tctacatccc attctcttct g 21 54 21 DNA Artificial Sequence Description of Artificial Sequence:: Forward primer 54 gtggtgaaca ccaataaatg g 21 55 24 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 55 aagcaaataa aaccaataaa ctcg 24 56 20 DNA Artificial Sequence Description of Artificial Sequence Forward Primer 56 ttggaatcaa tggagcaaaa 20 57 20 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 57 agctttaccc aatgtggtcc 20 58 23 DNA Artificial Sequence Description of Artificial SequenceForward Primer 58 gccatgtacc cacctgaaaa atc 23 59 24 DNA Artificial Sequence Description of Artificial Sequence Backward Primer 59 tcagaacacc cgtgcagaat taag 24 

What is claimed is:
 1. A method for screening for neoplastic cells in a sample, the method comprising: contacting a nucleic acid sample from a human patient with a probe consisting essentially of SEQ ID NO:9, wherein the probe is contacted with the sample to form a stable hybridization complex; detecting the formation of said hybridization complex, wherein an increase in the level of the hybridization complex relative to the level of a hybridization complex formed from a nucleic acid sample from non-neoplastic human cells is indicative of amplification of the sequence to which SEQ NO:9 has hybridized, and that said cells from a human patient are neoplastic cells.
 2. The method of claim 1, wherein the nucleic acid sample is from a patient with breast cancer.
 3. The method of claim 1, wherein the nucleic acid sample is a metaphase spread or an interphase nucleus.
 4. A method of screening for neoplastic cells in a sample, the method comprising: contacting a nucleic acid sample from a human patient with a probe that hybridizes selectively to a target polynucleotide sequence consisting essentially of the sequence of SEQ ID NO:10, wherein the probe is contacted with the sample to form a stable hybridization complex; detecting the formation of a hybridization complex wherein an increase in the level of the hybridization complex relative to the level of a hybridization complex formed from a nucleic acid sample from non-neoplastic human cells is indicative of amplification of the target sequence, and that said cells from a human patient are neoplastic cells.
 5. The method of claim 4, wherein the nucleic acid sample is from a patient with breast cancer.
 6. The method of claim 4, wherein the nucleic acid sample is a metaphase spread or an interphase nucleus.
 7. The method of claim 4, wherein the probe consists of a polynucleotide sequence as set forth in SEQ. ID. No.
 10. 